I'm not sure a colorless (black?) tag would avoid clashes, as the color of the text in the Threads Pane is the color of the tag with the lowest number, e.g. if a message has the Important (1), Work (2) and Personal (3) tags, the text color is red (1), no matter which order the tags are applied.

This may actually help at least for a while. I can add the colorless/black tags after the colored ones, so their black color becomes low priority and irrelevant when there is a clash with a tag higher up, or it will show as the default black when there isn't a clash. Thanks!

This should work for as as long I don't need to add a new colored one, because it will be listed as even lower priority and its color will never show in a clash with the black tag above.

Ideally, there would be transparent/colorless tags or we would be able to change the order to keep black ones always at the bottom.

Now the question if there is a way to change the order (without messing up the indexing).

There's a discussion of tag reordering here:

https://superuser.com/questions/1543390/how-do-i-reorder-tags-in-thunderbird