No problem.
Yes it's just a very tricky thing to work into an "all-in-one" tool like this without making it incredibly complicated, we already need to handle 5 display modes in 3 possible matrix colouring methods, so that's 15 possible configurations that each need to be carefully handled in most of the operations, adding 2 more colouring methods (per tile cell, per map cell) would raise that to 25.
Some kind of dedicated tool is probably the answer, one that can take a CharPad project, strip out any "per char" colours/materials and recompress, then allow free colouring/attributing of the map cells.
Ps. you might find some use from the existing "Export Colour Map" option, it allows you to export a "per map char cell" array of colour data (colour matrix data) regardless of whether the project is tiled or not.
See...
'Import/Export >> Binary >> Export colour map (per map char cell, CmLo)'.
'Import/Export >> Text/Asm >> Export colour map (per map char cell, CmLo)'.