It seems the containers in the corner room are all owned, so is there any way to store things safely there after the Debt Collector quest?

I wouldn't mind knowing this too. I just completed that quest as well. I usually make Novac home as its just the most handy overall, with the least amount of load screens.

Quoted from the wiki (same article):

"You can use this room to store items, and taking the items out of the desk(s) is not stealing even though the words appear red."

"Items in the room cannot be taken without being considered "stolen"."

"Neither desk is safe, so it is advised to store items elsewhere and only use this room for the "Well Rested" perk."

:huh:

You better make some tests yourself.