I included punctuation.definition.comment.gdscript in the comment part of my theme file and it now colors the comments, at least. Like such:
<dict>
<key>name</key>
<string>Comment</string>
<key>scope</key>
<string>comment, punctuation.definition.comment.gdscript</string>
<key>settings</key>
<dict>
<key>foreground</key>
<string>#967f75</string>
</dict>
</dict>
My only problem now is with not being able to toggle the comments with the shortcut keys. I've tried several possible regex combinations suggested around the internet for detecting python comments, but none of them worked. My guess is there's something wrong with the context definition for GDscript. I looked at the YAML-tmLanguage file, but once again I can't tell what could be wrong...