Different folder formats can filter out different things. I think it would be strange to enter a new folder in the file display area, have it trigger a different folder format, and then have items in the folder tree appear/vanish based no the format.
The tree could use the settings from the Custom format, or get its own Tree format, but I'm not sure it's worth the change for what it would add in configurability, and then the tree settings would be split into two places.