Hello, I'm new here but thought I'd answer your questions.
As far as I'm aware UOAR has a lot of little quirks as you describe.
I use a mixture of UOAR and in game editing to sort the problems out. Get Pandora’s box 2 to do the paintings and other thing in game. (Use nudge)
The houses made in UOAR are not frozen on the map when placed in game. You can nudge up and down tiles if they don’t fit and also you can change the hue etc. Remember PB2 or use [props
If you want to use an object that removes a tile under it, just dupe or [add a new tile and place the tile under it. This is when Pandora’s box comes in handy.
One annoying bug I have found is (I suspect) the foundation raises after saving and reloading. Change the level to foundation and delete it as soon as you start with a new building. This has helped me and suspect that’s what your disappearing object bug is.
Also remember to [freeze the building when your happy with it. Else you may find your building will decay (not time out but run out of memory or something.) when you build more buildings and use more and more objects. It also puts the building on the radar
Have fun.