Hi, Jaskim08 and all.
As for factory fitment on vinyl tops for the later Town Cars, I have been wrong in the past and will probably be wrong again. I'm trying to find references on this, but haven't been fully successful one way or another.
The first "reference" to prove one way or another, which I haven't gathered yet due to cost but others here probably have would be the Lincoln printed dealership brochures for each year. If a vinyl top was available from the factory, at least one car in the brochure for that year will have one.
Your parts supplier listing a "factory" top available for the 2003-2010 model years would strongly suggest that Lincoln had brought them "back" for a few years due to "popular demand." If that's the case, but you still want a "factory vinyl" roof for your 1998, then there is still some hope for you.
And "dealer-installed" does not necessarily equal garbage or even undesirable. After all, if nobody wanted vinyl tops, then the dealerships wouldn't dream of putting them on their cars. They want to sell the cars, after all, and won't do anything to them to make the harder to sell.
In the end, unless you are actually trying to maintain or restore your Town Car to concours standards, it doesn't matter all that much. The dealership tops were common enough that you shouldn't lose points for having one installed if it's in good condition. And a true factory vinyl top, with provenance, will be even better. So, vinyl or steel if you want too, just keep the car itself what a luxury car should be.
This controversy can run both ways. The 1969 Lincoln Continental Mark III came with a vinyl top as standard equipment. However, there was a "vinyl top delete" option that wasn't free, that a little over 700 customers paid for and had delivered. So, if you have the provenance, you can win full points at the concours with your painted roof Mark III.
As a final comment, my 2001 Town Car has a "fabric texture" vinyl top. The top is intact, and looks nice, whether it was installed at Wixom or a dealer body shop in Michigan, where the car was delivered to its first owner. Removing said top isn't at the top of my maintenance list, or even on the first page.
Cheers!