Yes, the shared documents would be visible in the clients intuit link account, which I don't think would hurt anything.  I do believe the documents have to be here in order to be importable. I think you can still upload documents here without having to invite the client to Intuit link, so I think it still wouldn't hurt anything.  

It appears the firm documents section is new, which is why there is not a lot or resources for it yet.  However, my understanding is it will accumulate things your firm creates for the client (ex. Transcripts, pulled through Pro Connect, or Tax plans created with Tax Advisor).

It will be interesting to follow as more resources and uses come out!  Thanks for posting the original question, hopefully it nudges ProConnect support to address it.