Yes, that is by design. The colour value default is set in Document Settings and inherited by (container) notes via $MapBackgroundColor.
On the first point, I’m less sure. I think the issue is that the highlight uses a ‘tint’ (a shade) of $Color for the highlight. Here, ‘bb’ is the current selection:
Notice that the default ‘dark mode’ colour scheme sets outline text title to white. So if I set ‘bb’ $Color to red, is not too evident:
but if I untick ‘white titles’, the selection is clearer:
Indeed, if I reset bb’s $Color to ‘normal’:
It’s less clear but at least better than with white titles.
These nuance of UI shading and the way OS dark mode works are, I think still bedding in. Anyway, that’s how things are at present. If you think different configuration methods are needed you could make a feature request. A problem for the designer of a toolbox app like Tinderbox, compared to a one (or few) task utility is that not all users do the same thing or set up the Ui the same way so ‘good’ defaults can be hard to decide upon.