Would it be any better to have a symmetric airfoil on the bottom in place of the flat bottom airfoil? I would hate to have to get rid of the element that makes this so iconic. I'm not really sure I fully understand what you mean by saying air dosent scale? Would you make both the vertical and horizontal bigger?
Tail areas also seem fine using the TLAR method.
Air does not scale: The density and viscosity of air does not change whether you are using a full-scale or 1/16 scale airplane. The thought is that if you use the same aerodynamic features then generally they will fly the same. However, there are still size constraints because of the physical size of the volume of air. For your wheel struts, you have these struts that have an airfoil. The air going over the top is accelerated per standard principles of aerodynamics. Now, the length at which that accelerated air extends away from the top surface of the strut is determined by your chord thickness. To add a bit of insult to injury, the extreme dihedral of the struts allows for the air extension perpendicular to the upper surface to conflict more with the two different panels and will create a larger pocket of turbulent air... all under the main portion of the wing. If you are creating turbulent or accelerated pockets of air under the top wing (and a vast % of it at that) you are likely to get a lot of issues with pitch control that may be perceived as a CG issue.
It may be that you are seeing OK evenness of lift at one angle of attack of the wing/struts but when you change pitch, roll, or yaw the angle of attack along with variation of span-wise flow of air is going to disturb the air on the bottom of the top wing.
Another way of looking at this section is to think of it as an annular wing. Annular wings almost always have constant chord length. The intersection of the strut and the main wing is an instance of change in chord length where the flow of air is creating an area of the top wing that is becoming ineffective.
I'm not an expert on these things. Perhaps
@Mid7night may have some thoughts on this more but it is an interesting subject of discussion/debate. The fact remains that it's such a good-looking model that it should not be left to the wayside.