Mutter incorrectly draws the drop shadow behind the windows itself. For transparent terminals and the like this means looking through the terminal right on the shadow, therefore transparency does not work as intended.
This is already solved in the git repository.
I took the patches from https://bugzilla.gnome.org/show_bug.cgi?id=635268 and incorporated them into the ebuild.
This should fix the issue until 3.0.2 is released.
Created attachment 273131 [details]
new ebuild including the transparency fix
Created attachment 273133 [details]
Created attachment 273135 [details, diff]
Created attachment 273137 [details, diff]
Created attachment 273139 [details, diff]
This is now fixed in the overlay, thanks for reporting!