The new tabs feature along with the toolbar as of now in windows 11 is not skinnable. It will be semi transparent and out of place on mist styles. Something we cant really deal with. Only way around it is using explorer patcher to get rid of that feature. Here it is on my XP theme and another theme I tested with from the gallery.
Other than that the dark mode feature added to WB11 will destroy any themes its enabled on unless they have support for that mode. If a theme does not supply dark mode features, it will darken everything for that mode and destroy the entire look of said themes. You would need to turn that feature off manually in advanced settings so that it will not do so.
Other than that, all themes will apply fine and work as in tended on windows 11 minus some new stuff they also added to WB11 that does not affect the current themes.
The darken on your subline text app is because you told it to request a dark theme. WB gave it exactly what was asked of it. Without WB the titlebar would also look different in that mode. The issue is some apps ask for a dark theme and then work on a reasonable assumption that the colours are dark and so can use white text. If the app is set to use a light mode theme (which seems to leave the background dark anyway in that app suggesting the option only controls what it tells the OS it wants) then WB wouldn't darken anything.
Users also tend to complain if they have an app in dark mode and then buttons, menus etc are blindingly bright as they asked for dark mode.
Obviously not a problem if the skin is already dark hence the change in beta 2 to only enable it if the skin isn't dark already and also up the contrast of darkened parts and offer user control over this.
With regards to the tabs, it very much depends on the skin. If a skin used the glass sections of per pixel frames then it would probably look reasonable. This is because there are frames for normal and frames for when the skin uses glass which is whats under those tabs. So the skin doesn't need a line between the caption and the rest of the glass. Skins like corporate included with WB show this and look great.
The skins with issues with the tabbed explorer probably also had issues with Internet Explorer, FireFox and Google Chrome as they too overlap tabs with the titlebar
There is possibly the option in the future to have different frames in use for those windows with tabs. Obviously wouldn't help old skins, but new skins could if they wish have a different look for those particular windows to take into account the tabs will exist.