Yes, a great deal of difference.
I learned from my years in aviation that there are several things in life that we cannot scale to suit our liking: water, fire, smoke, and air.
If you ever seen those early pre-historic (Internet) sci-fi movies, like the cult Godzilla series, you will notice that 'buildings' that are on fire looks odd. The flames looks ridiculously outsized for the 'building'. That is simply because we cannot scale
DOWN the flame to the proportion of our scaled
DOWN building. Same thing with water where waves from wakes looks ridiculously large for a 'tanker' in motion. Special effects are much much better today because we are able to scale up or down those four items through computers.
Any way...The only purpose scale down models serves is to confirm the basic air flow behaviors over the basic airframe that will allow it to fly and remain airborne. Because we cannot scale down air molecules and aerodynamic forces, small features can be 'ignored' by air flow and those small features can affect air flow in unexpected ways on the real much larger airframe.
NASA - Wind Tunnels at NASA Langley Research Center
Notice the highlighted.
In order to simulate the same air flow behavior on a 1/4 scale model as the full and theoretically real aircraft, we would have to pressurize the chamber to 4x atmospheres. This means a simple wind tunnel or open atmosphere flight of the scaled down model would not give us any accurate assessment on how the theoretically real aircraft would fly and behave, especially in maneuvers. All it does is say: 'Yep, this thing is shaped just good enough to get airborne.'
Even so, we still need the real aircraft to actually fly with all sorts of measurement data in order for us to say our new aircraft is production worthy. That is why we have test flights and test pilots. And then, problems can still come up well after the aircraft is in production or the production line have been closed.
Example...The F-18 developed stress cracks at the vertical stabilators' roots. Several F-18s were sent back to more wind tunnel testings and structural modifications installed. These were not revealed under scaled down model testings during R/D and production.
The bottom line is that scaled down model testings can only guide us so far. An aircraft is much more a complex structure -- aerodynamically speaking -- than most people realize. And the more sophisticated the design to do multiple and complex tasks, the longer it will take from paper design to full production. As in ten yrs or more. And a lot of money to boot.