I wonder what's driving you to continue using CapboardSet when this plugin already has a list of authorized players and unifies the style of the rest of the features. Maybe the favorite icon isn't checked? I assume it's to highlight the TC Owner? If so, I can make a note to add it.
The problem with the CapboardSet interface overlapping BetterTC must be due to the plugin's overlay configuration. It seems to automatically display when opening TC, and due to its configuration, it overlaps.
Regarding point 4, you get the message "Upgrading to this level is blocked" because a check is made to see if any plugin is blocking the upgrade grade. For some reason, IQGradeRemove is blocking it and canceling the BetterTC upgrade. Maybe this plugin uses: OnStructureUpgrade
You could try editing the plugin and adding or changing this line:
string[] incompatiblePlugins = { "BuildingSkin", "BuildingSkins", "XBuildingSkinMenu", "IQGradeRemove" };
With this change, BetterTC won't check OnStructureUpgrade. If this fixes the problem, I'll have to add this so it doesn't cancel the operation.
Regarding point 5, I need to investigate whether it's possible to fix this. I'm afraid it won't be easy since what my plugin does is override the game's removal system that removes and blocks external wallpapers. Perhaps by removing this, they sometimes generate (for some reason) and that's why they're visible, because there's no system to remove them.
Regarding point 6, I also use UbertTool. I just tested it on my server and the building blocks have improved. Since the ownerid of these blocks is mine, then it detects them as if they were really mine.