I believe I've figure out a good way to turn 64x64 terrain sets into 96x96 terrains usable by Tiled with a 32px grid. It takes a bit of legwork, but can generate files which are very easy to use once you get going, and make heavy use of Tiled itself in order to do this.
First you take your RPG Maker formatted files, and open them up in a new map with 16x16 tiles. For each 64x64 bit of terrain take each quadrant and stick it into the corners of a 96x96 space; you'll have an empty plus sign in the middle. Then fill in the empty spaces with the appropriate pieces, but note that you'll have to flip up/down, left/right in order to get the texture to loop correctly. It's tough to explain in text, but in the center, bottom-right becomes top-left, top-right becomes bottom-left, etc.. On the outside spaces, you just need to flip either left/right or top/bottom.
You'll need to do this for both a patch of terrain with corners going out (convex) and corners coming in (concave). There will be at least one patch which can be discarded it seems.
That's the tedious part, but when you are done, you'll have a "map" of a tileset you can use with Tiled. The next step is to do the "Export to Image", (don't export gridlines or grey background) and you'll have a new tileset appropriate for use in a map with 32x32 tiles.
The best part is that once you've done this for one RPG Maker layout, say A1, then you should be able to replace the tileset image with A2 and the translations will already be done and you can save it as another new tileset.
I'm just getting started on this work for myself, but when I am finished I may be able to share my .tmx file so you can convert other files yourself.