Server-based SharePoint integration and resource throttling issue

If I integrate CRM Online with Sharepoint through server-based Sharepoint integration, I need to take into consideration Sharepoint's Resource Throttling limitation.

A document library with 5000 or more documents might experience resource throttling. https://technet.microsoft.com/fi-fi/library/dn792527.aspx

When Sharepoint and CRM are integrated, each entity that is enable for document management gets their own document library in Sharepoint. Does this mean than that if I would e.g. have more than 5000 accounts and for each account I would save one document in Sharepoint, I would experience resource throttling issues in CRM. Or would it only apply if I had 5000 documents saved for one Account. What is scenario in CRM where I would come across this issue?