The distinction the clerk is pointing at is real and it turns on state law, so the specific answer has to come from a landlord-tenant attorney in your state. The mechanism is that most states define who gets the protection of the residential landlord-tenant act, and lodgers, guests, and occupants of transient accommodations are frequently carved out. The factors courts look at are the length of stay, whether the occupancy is by the day or week versus the month, who holds the key to the room, whether the operator retains a right of entry, and whether services like housekeeping and linens are provided. Services are one factor among several. They rarely decide it alone, but they're the factor a clerk can see on the face of your paperwork.
The part that's counterintuitive: being outside the tenancy statute is not automatically faster. Some states give innkeepers a summary removal path with police assistance. Others leave you with no statutory process at all, which means an ejectment action in a higher court, more expensive and slower than the eviction you filed. Find out which one you're in before you decide whether you want to be classified that way. Do not remove him or his belongings yourself on the theory that he's a lodger, because self-help removal is where operators pick up damages claims.
The blocked bathroom is a separate and more urgent problem than the arrears. Your license almost certainly has habitability and fixture-count conditions, and a bathroom made unusable for five paying residents is a condition violation you own regardless of who caused it. Document it, notice him in writing, and clear the obstruction under whatever your lease says about common areas.
When this resolves, have counsel look at whether the services are worth the classification ambiguity. Linens on request buys you very little revenue and a lot of uncertainty about which court you're in.
