Currently the environmenttable that you see when you install/update adds some classes that are used to style some text red/yellow/green to indicate what level of problem you're facing.
These styles aren't used anywhere else in moodle, which makes them hard to theme. Well not hard to theme, but rather hard to remember to theme as they're only used in the obscure corner of the site.
It seems that they are currently aren't styled in base or canvas, or any theme derived from them.
For the themes that do actually style them, it's a bit of a waste sending those styles to every user of the site, since they'll never get a chance to use them.
For bootstrap derived theme the obvious thing to do would be to use the standard Bootstrap styles for this task (e.g. label-warning and text-warning etc.). Currently the Clean theme uses some less to map these styles to existing classes but it would be simpler and easier to just output the correct classes in the first place.
Separating out the presentation of these messages from the complex logic used to generate would allow themes to wrap these messages in whatever HTML they felt was appropriate.