@Hinato: When I first read your post I was skeptical if it was possible to make square rooms on hex grids and make it look good, so I tried it out myself and was surprised at how well it worked. I never intended for this in the toolkit, but it works with very little adjustment. If I understand you correctly you were trying to do something like this?
If I’m reading your post correctly I suspect that you may be mixing up the visual representation of the walls with how edge costs (walls) are stored in the various grid arrays. If you place a wall on a tile and resize it by increasing its scale the toolkit will still only register the tile you placed the wall as a wall. You have to either place a separate wall on each tile (as I have done in the screenshot above) or you can represent the wall as whatever mesh you want and place invisible walls on each tile. In the screenshot above I have used the regular wall tiles. The center wall two tiles behind the pawn won’t snap in the center of the hex by default, so I ignored Snap to Custom Grid and placed it appropriately.
Edit: Still, for this kind of stuff I think your best bet is to create your rooms with regular meshes and use invisible walls to modify the edge costs. The wall tiles for square grids are a pain to line up properly on hexagonal grids. Adjust the edge cost variables of the invisible walls to 0 for all directions you don’t want to be able to enter the tile from.