1- The reason is to have more options. Iran also had some talks with Russians for a similar deal. Basically these systems need ground stations around the globe to increase their accuracy, and Iran wants to have ground stations for Beidou and Glonass in Iran. The problem being Iran can not entirely trust GPS and Galileo to be available since if the West ever tries to shut it down or degrade the service for Iran, then Iran will at least have two more options with some minimal stakes in them (the ground stations).
2- You can to this problem with all of such systems not only Glonass and Beidou but also with GPS and Galileo, and not only the encrypted signal but also civilian. After all this is someone else's system and not yours.
3- I would not use those terms you used, but at the end of the day, we have to accept the fact that we do not have the technologies in many areas. And the reason for that being our backwardness in STEM. So either we will have to depend on someone else whether US / China / Russia or develop our own.
4- Not that we can design and manufacture the chips either but even if we could, still it would not solve the problem since chip is only the receiving part. The actual system belongs to someone else and if you do not have your own then you are basically on your own.
If things were that easy as you say. When was the last time Iran designed and built an atomic clock or autonomous systems required for building such a system? In addition to these, Iran has had trouble with its SLV program too. One option would be for Iran to design and build its own regional positioning system which other countries are also doing for example India, and augment it with as many available global systems such as Beidou, Glonass, GPS and Galileo. But for this, Iran must at the very least develop technologies, it currently does not have, eg. the technology for atomic clocks, the heavy lift SLV and reliable autonomous systems.
And the military side of this though important on its own is not as important as its civil applications. You must know how much a modern economy is dependent on such systems from trucking to civil aviation and from automatic inventory systems to safety services. Iran needs and has to learn to concentrate on civil application of science and technology before its military applications. And there is no shame learning it from China when US or EU will never cooperate with Iran in this regard and when Iran's total R&D budget is just a few small billion dollars.
There is nothing in the news that says it. The website of the company refers to civil applications of it. But even if there is some agreement, they can not publicize it since the military sanctions are still going to be on Iran for next few years and this being a military product can not be sold to Iran.
Of course it will help with navigation of the UAV's, but Iran has been using open signals of GPS for that since a long time. The main problem for Iran's UAV program is the lack of satellite communication links which allow to operate a UAV beyond line of sight in great ranges. Another problem is to develop technologies such as contrast lock or scene matching, millimeter wave and semi-active laser technologies for small and cheap enough guided missiles.
Let me answer your points in reverse order, but before all I like to say no one says go and develop it now. What I am saying is that there is no point working with Chinese and paying them hundreds of millions for BeiDou when it is a copy and paste of GPS and Galileo (I can tell you exactly what they copied from where!) That is Chinese typical attitude. In Optical networks they copied Ciena technology and stole their IP, in the rest of the technologies that are crucial and strategic they do the same and then flood the market with cheap designs and products! This all done with the backing of state and military! ZTE, Huawei all are the same. By the way same Huawei and ZTE destroyed Iranian digital switch technology. It is treason working with them. I was told by my Chinese manager to copy the Synchronization from another vendor with the blue prints! Of course I didn't comply! So what I am saying is form experience! I am neither a diplomat nor a PDF and this is my experience. Now back to the topic, IMU/INS integration and aggregate systems is my job:
4- Chip developments not an issue if the system belongs to someone else. You use available chips or IP's and they are all over the place for the existing ones.
3- I don't agree on STEM part. We have well known figures in Geomatics for this purpose besides as said the technology for such systems are well known. Best thing is to spend million dollar and have the Geomatics brains that one even published an encyclopedia define a road map before jumping in the wagon with Chinese!
2- For Civilian purposes there is no issue using any of the systems available now. A combination of GLONASS and GPS ensures good reception on all inclinations on the globe. You can add BeiDou but it doesn't add anything new unless Chinese use the allocated frequency sooner than Galileo.
1- Yes, Specially the Russian one due to its method of GNSS. Ground stations calculate satellite positions, synchronize frames, correct for ionospheric error and gravitational error if it is an option for the station and upload information to the satellite. All of them need such stations. Now the question is, which one is cheaper and more reliable.
Regarding the clock:
Galileo has the highest precision clock on board, "Hydrogen maser" and (GPS, BeiDou) use rubidium clocks while GPS and Glonass use Cesium clock. As far as I know, usage of Atomic clock can not be restricted or blocked. I don't think that would be an issue.
Regarding the SLV:
Once again not that go and do it now, the point is no need for it use the existing ones. If crucial and strategic then Chinese are no different to Russians and everyone else on this matter. But on SLV you can have India or Russia send it to space.
Regarding the civilian use:
Exactly for civilian use there is no limitation for Iran. Regarding the R & D both Europeans and US will cooperate so will Canada, if there is a will on doing it. Where do you think all our Geomatics minds have studied or worked? This is not the reason for cooperation with China on this regard. For civilian purposes no one restricts Iran.
At the end, working with Chinese and Russians on this regard is not necessary after the deal if leader knows how to behave and dosn't bite once in a while) The technology is mature and old. The SDR (software defined Radio), Geomatics, RTL and electronics and the RF design for GPS frequencies (~1xxx MHz and max 20 MHz BW ) all is in hand and it is an opportunity to define the project and have Iranian young engineers learnand spend the 200 million euros or dollars that you want to give to Chinese! if necessary! (keyword is if necessary)
If you get free ride from Chinese go for it. If they offer cooperation at reasonable price then it is good why not. But Chinese never offer anything free and usually take more than they offer. That has been their attitude everywhere and specially when dealing with Iran on all projects!
The reason Chinese went for BeiDou is not that it is better! No it is cut and paste technology and inferior in accuracy to US recent 20MHz bandwidth. It is because then have the money and they can and they need to be independent in this technology and the precision they get is sufficient for their purpose! If Iran wants to be independent then BeiDou doesn't offer that other than that use the existing ones avoid paying the Chinese R & D!