Excellent suggestion Quintillus! And you came up with it without even installing the extension. Impressive!
I have actually thought about this in the past. But I was trying to come up with a good way of putting it into the UI without making it too complicated. There is already a way of adding the same abbreviation to other domains with one click when you try to add the same abbreviation to another domain but it doesn't completely solve the issue and like you say an intermediary level abbreviation designation is needed.
So after thinking about this for a while, I came up with this plan (which is pretty much what you are suggesting):
I will add a new menu item called "Assign tags to this domain" to ABBREX main menu. When you select this menu item when you are on civfanatics.com for example, you will be able assign tags or subscribe to tags if you will (there will be an autocompleter based on existing tags helping you out of course). When you assign tags to a domain and you visit that domain with ABBREX, you will see abbreviation meanings for:
1) All generic abbreviations
2) All abbreviations specific to civfanatics.com
3) All abbreviations with tags civfanatics.com subscribed for (Civilizations, Gaming, Strategy for example) regardless of domain.
Since people already add tags to abbreviation meanings when they enter them, tag assignments for domains meshes really well with the existing abbreviation tag system.
I will also put some convenience buttons on the "Add Abbreviation" form to let users easily transfer tags from an existing domain-specific abbreviation to a domain without having to type.
I already started working on this so I'll probably have it on the next version. Let me know what you think.
By the way, I made ABBREX installable from Firefox 3.6 so if you'd like to try it you can now. However, I never tested it on 3.6 so it might not work so I have to give you fair warning.
Firefox 3.6 support ends in April 2012 so you might want to upgrade anyway. The new versions aren't so bad.