Hi,
Yes this can be a problem when editing tiles using "Per char" matrix colouring.
The tile editor has a '?' button explaining a solution, ie. you can just click with the middle mouse button on a tile cell to instantly select the pixel colour and the character in the set, this loads the pen(s) with the matrix colour(s) for that cell so you can paint with it/them + if you change the matrix colour(s) it will only affect that one cell/char.
Auto-selecting the first char of a clicked tile may help slightly but is not really a solution.
Thanks for your feedback though, I will have a think about it.