Don't worry asking questions, I really appreciate them! They tell me that you guys like my stuff :)
My plugin does not add a "new" layer, that would be too complicated. Instead, I designed it to follow RPG Maker's 6 layers world (i.e. A lower, A upper, B lower, B upper, shadows, region tiles).
I briefly tested this pattern, and it worked for me. I was able to first build the window (line 6), and then the flowers (line 7) on top.

Tell me whether this fits your needs!

