Add an extra tab to the palette which will be made up of 2 autotile formats:
1. Similar to A1 (animated)
2. Similar to A2 (typical autotile)
Drawing from this tab will place autotiles on one of the UPPER layers. The tiles could have rounded corners with a transparent background, and the passage settings would allow O, X, star, or the old square from XP days (you can walk around on an area covered with the tiles, but you can't go over the edges).
I had this working in the earlier MV versions, but after the rewrite of the tile classes it wouldn't work anymore and I haven't had time to look at fixing it.