Hey, what you think, man? I did it on purpouse!!! 
Just kidding... However... I think that use is great!
Another bug I found right now is that when you click on a concept, it shows every concept in the database that match that concept, no matter what course it belongs nor if the glossary or entry has the dynalink setting enabled... Neither take in count the case sensitive setting when showing the concept
Just fixed right now.
Will
Mixing your suggestion with a thought.. what about if I add a new setting at glossary level (not entry level), let's say, GlobalGlossary, that means that that glossary could be linked from everywhere no matter which course it belongs to...
This way... an admin could add a glossary to the main page, hide it (or not) and make it avaible globally.
This settings, I think, should be enabled only by and admin...
Any comment?
Yes, yes.. fries and coke too!! hehehe... Just kidding my friend... I liked the enthusiasm shown on your post
What you meant by "main and secondary options"???
The blocking feature I think will be difficult as the parsing is made by a global function what didn't know where is it called from... Perhaps Martin or Eloy has another solution.
This overlaps somehow the request to stablish that some modules does not use the automatic linking at all.
Will
What you meant by "main and secondary options"??? 
