i am currently working on a custom map and noticed that the TILEABLE TEXTURES that you paint layer by layer have a mismatch between what the Editor is showing and how they look ingame.
Specifically, they are larger Ingame compared to in Editor. That also changes the alignment of tile seams.
I noticed it because i had placed some decals to sit neatly inside blocks of stone that are part of one of the tileable texture layers. Ingame the alignment was off, but as you very clearly see in the attached screenshots, the decal did not move, the scale + alignment of the tileable texture changed. And if you look closely at the circular base of the center hill, you will see it affects ALL tileable textures.
In Editor screenshot: