I think they were an issue, the EU version of the game had all but one two removed, the one we still have now in GT5/6 and another one.
The one we "still" have now, the pure fantasy Formula GT, is from GT4 and not GT3. All of the classic "fake" F1 cars from the NA version of GT3 were removed and replaced with the two modified versions in the EU version, and all models were effectively removed entirely in the jump from GT3 to GT4. I assume that's why they made the FGT to replace them.
And anyway, it looks like there are small differences on the 001 and 002 from their real life counterparts. The 002 is definitely still the MP4/4, although I can see they changed the front wing a bit (different endplates and the curvature of the back/top of the wing is similar to the MP4/6) and the rollbar is slightly different. The 001 looks to be the FW17 from 1995, albeit there might be some small differences as well (one being the nose posts that hold the front wing are much closer together). It looks a bit like they might have just pasted the newer bridge nose from the '95 model onto the F094/H but then again the FW16 and FW17 were very similar models anyway, other than that one new major change. And the 001 does have the lower/wider rear wing that was introduced in 1995 rather than the taller and narrower pre-95 wing that's on the F094.
Anyone have a guess on the year the formula for the Formula Gran Turismo is based on?
Closest year would be 2004 but they didn't quite emulate the existing models. They share a similar general look and used some similar elements, like the aero winglet pieces on the sidepods, but the FGT was designed to be its own car. Particularly the front nose isn't quite like any F1 model we've ever seen and is instead more cylindrical rather than flat on the top like typical F1 cars from the period.
But I agree it looks like the Williams since it has the Rothmans looking decal.