lately I switched to Win 10 and while that (at least Win 10) I figured that windows is displaying no more than 11 over icons.
Additionally Win 10 is reserving the first 5 slots for his onedrive which is a pain to get rid off... (with Win 10 Home is seems to be impossible

Which means that for my applications there are only 6 slots left. It is way too less. As a developer I use Mercurial as my Repo which by itself needs already 9 overlay icons in total. And of course I have some over tools with overlay icons.
My suggestion would be a feature for TC which displays overlay icons independently from windows - displays all of the overlay icons or a predefined number. The total count of registered overlay icons are stored in the registry - so the information is available. But like i said windows is just picking the first 11 to display.
They can be found via this path:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\ShellIconOverlayIdentifiers