Well I was asking for this feature because you know, “if you don’t ask, you don’t get” 
I agree it must not be a simple one but it would be very useful.
Some feedbacks on the interesting challenges you mentioned :
Ideally all items would still be suggested, because the first intent of this feature is to add a link between two entities, so the user need to be able to search for any item. I think otherwise I would be confused not to find an item, whereas I can find it in all other places via “search / #”. If the added item doesn’t show up then because of the filter, maybe a warning message could show up just as a reminder of the filter. This way the feature remains coherent with the rest of “referencing” features.
Ideally the filter only impacts the display, not the actual linking. That way it would remain coherent with the current filter feature on boards (= if we use a filter on board, it does not unlink items).