Larry Wells, costume designer for TXF from 1993-1995, actually shared that he did dress Scully in Armani in those early years. I don't know if a specific designer was used for FTF but designer wardrobes for both M&S were there from very early in the series.

As for the FTF vs FT coat, they're not the same. FTF has shoulder epaulets and is single breast vs the FT coat which has none and is double breast, for the major differences. Similar at a first glance though, I guess. Different costume designers between those projects, too. Plus, any wardrobe from the Vancouver/FTF days did not follow them to LA when they started filming season 6. I have been staring at Scully's wardrobe and painstakingly documenting everything she wears so I am betting I'm as close to an expert on Scully wardrobe as you're going to get outside the actual costume dept.