Yeah. The best way is probably to cut out each tile (or each *section* of an autotile), run it through Waifu, then resize. Long process. Haven't tried it yet. You may still have to clean up the edges, though. Doesn't really seem like resizing old tiles is worth it.
That also causes seams, yeah. I've come up with a method that works pretty well. With some tweaking it could probably give very good results - at the moment it's useable but I'm still tweaking.
EDIT: Here are some pics of my current results.
Firstly, naïve Photoshop rescaling (seams are really bad here...):
Nearest Neighbour (better, but really fuzzy and generally blegh...):
Here's my current algorithm's attempt:
It's not quite perfect yet but it's getting there! (Also some of the glitches are actually present in the original tileset, if you compare the nearest neighbour rescale to the special algorithm one...)
Bearing in mind a skilled mapper would know how to tweak their map to get the best out of it (rather than randomly throwing down tiles to show a worst-case scenario), I think this could give usable results and unlock a wealth of old assets for devs to use.