I dont know the mk 3 or about paint around windscreens. But mention of bubbling and yellowing paint around the sills brings to mind stonechip paint as applied at the factory. This tends to have a bumpy finish, sort of orange peel affect,. Its often overpainted in body color, but the protective stuff itself is often white, grey or yellowy cream colour. Is it possible the white overpainting has come off exposing just the stonechip coating as a yellowish tint? This layer will itself be on top of the original car body paint applied at the factory. so the paint finish may not yet be breached and liable to rust.
I dont know if the Mk3 is the same but my white mk4 has a very thick application of stonechip, almost like rough cast rendering. On other cars it was more like orange peel.
I am also intrigued that the application of your underseal seems to differ from side to side. Is it possible the area was repaired at some time in the past, perhaps because of damage when a jack collapsed? The original stonechip may have been buffed away and not renewed. In these circumstances there is always the possibility that the new priming and paint applied is less durable than the original factory finish.
If there have been repairs you cant really speculate in theory about how it compares with factory original paint. . You would have to be there and examine it in detail. If you are unsure a friendly independent body shop might give a quick opinion, although they might be biased towards more business. And even then, short of rubbing paint, underseal, under paint, primers and any filler back to bare metal you cant be sure, Or that the repainting will be any better. If it looks basically sound then maybe a new coat of stone chip , or simply overspraying the existing exposed stone chip may be all thats needed.
But of course without being there or knowing your exact problem I may be talking nonsense
some photos of each side might help.