IMO this should not be a black and white solution.
Ship size should be a factor in the spectrum between Aircraft and Brick which could also have gameplay benefits.
The interceptor for example could be one of the most agile and best performing in atmo, but a corvette or destroyer would be much more limited. I suppose the in-lore handwavium could be it is harder to shape the shield over a larger object? Smaller ships would be designed to function well in atmosphere regardless of their shape because of basic necessity (human transport, local planetside economy etc).
So my opinion is to design for realism but then fudge it for the smaller craft to fit gameplay.
If you have large ships that look like bricks but behave like 747s then you immediately generate an inauthentic experience. Designing for a realistic atmo model might also benefit future expansions where other factions have more streamlined large craft (ie. better for atmo vs space.). Instead of later retrofitting a realistic experience over a “faked” model.