When you drag-paint something, be it a tile-set, overlay or whatever, you have to Ctrl-Z for every instance that particular thing was created, so just painting a very small area with a LAT, you'll have to Ctrl+Z dozens of times to undo everything (including each instance where you happen to paint over the same tile with the same type of LAT). It would be more convenient if Ctrl+Z undoes everything between when you clicked down the mouse button, to when you released it. Or if that doesn't work perhaps if you hold Shift+Control+Z it undoes the last 5 things.
When you drag-paint something, be it a tile-set, overlay or whatever, you have to Ctrl-Z for every instance that particular thing was created, so just painting a very small area with a LAT, you'll have to Ctrl+Z dozens of times to undo everything (including each instance where you happen to paint over the same tile with the same type of LAT). It would be more convenient if Ctrl+Z undoes everything between when you clicked down the mouse button, to when you released it. Or if that doesn't work perhaps if you hold Shift+Control+Z it undoes the last 5 things.