They're three separate systems and they can each independently kill the deal, so it's worth keeping them apart.
Zoning and occupancy is local. Many municipalities with campuses cap the number of unrelated adults who can share a dwelling, commonly at three or four, and some require a rental license or a specific rooming house permit above that count. The definition of family in the local code is what controls this, and it varies by municipality, not just by state. Read the ordinance for the specific jurisdiction and ask the zoning office in writing whether four unrelated tenants on separate leases is a permitted use at that address. A seller telling you the house has been run that way for years is telling you it hasn't been enforced, which is different from it being legal.
Insurance is a carrier and form question. Your agent's instinct is reasonable, since a standard landlord policy contemplates one lease per dwelling. Separate leases per bedroom can push a property into a different classification with different rates and exclusions, and some carriers won't write it at all. Get the classification and the form confirmed in writing before you close, and ask specifically how liability is handled among tenants who don't know each other, and whether the carrier requires each tenant to carry renters insurance. Many operators require it in the lease and track it, because it moves small claims off the property policy.
Licensing in the sense of a real estate or property management license comes up when you manage property you don't own, and where that line falls is a state question. If you own it and self-manage, most states don't require a license, but that is a state-by-state answer and a licensing attorney or your state commission should confirm it.
What gets missed in this list is fire and building code. Bedroom counts that exist on the rent roll sometimes don't exist legally, a basement room with no egress window being the classic one. Four beds where the certificate of occupancy says three means your rent is 25% overstated and your insurer may deny a claim tied to the unpermitted room.