Thanks for the clarification, Eve.
I think I got it now and it would be a completely new approach:
- Replace the limited RefGUIDList with multiple RefGUID tags.
- Pull them into the profile's Properties using your technique.
- Find ways to add/remove RefGUID elements (via AddinBroadcast?)
I like the challenges EA raises... 
Ok, as a final summary to the readers I have taken the challenge and after a lot of struggling managed to replace the RefGUIDList with multiple RefGUID tags.
Using EA_OnNotifyContextItemModified() the GUID of the tags will be adjusted after creation.
Deleting a property is done in the built-in Tagged Values... dialog by selecting <none> for it and let the following EA_OnNotifyContextItemModified() callback remove the now empty RefGUID tag.
The key was to let the EA_OnNotifyContextItemModified() callback do all the housekeeping around the tags.
Unfortunately there is now a tight coupling between the profile containing the RefGUID tags and the EA_OnNotifyContextItemModified() code.
I wish this would not be the case but haven't found a solution.

But anyways: The RefGUIDList limit now is gone!