First, you should enable the "Draw Tile Boxes"

This is good for debugging since you can see the tile boxes. Disabling this might increase the map load time by a small fraction ( for large maps ) since it won't draw them, but I honestly saw no difference in load time with it on or off.
Then once you hit play test, I noticed half the screen had 48x48 colliders. So I checked the tileset, and the invisible / clear tile isn't still isn't set as passable. Once I changed that and hit play test again, it was all fine.
As for region boxes not working, you need to enable the region boxes parameter:

Enable that and test it now.
Although when testing that I noticed it wont place a regionbox if that tile doesn't have a tile ( you resized the map and didn't fill it with anything ). So fill the whole map with the clear tile and it will work fine.






