As a flightsim developer (albeit mostly panels, sounds and flight dynamics) I know that in any sim there has to be compromises unless you want to make one so vast in computing terms as to be almost unuseable.
Most 3d surfaces are made of enough polygons to give (for example) Port and Starboard sides so seperate textures can be used for logos, names etc. to make them always appear correct. A flag is usually made of a single (zero width) polygon and textured once. Obviously it will on occasions look wrong but it is a small part and it ain't usually worth making it a very slim 3d framework and using 2 texture sets.
BTW is it still correct to say that the UK Union Flag only becomes the Union Jack when flown from the jackstaff of one Her Majesty's Vessels? (Picky I know but similar to the way most people still refer to wing mirrors on cars when nearly all are now door mirrors).