As much as I don't trust her
this conversation has merit if we apply it to the real world.
A minor living in with an adult who's not her legal guardian/family member is illegal and especially not safe for a child
(yes we know MC is a great guy, but let's say you didn't know the MC at all, I'm sure he would have been cancelled immediately for "grooming" or something of the like)
The manager is actually in the right for asking her about her situation and how long she plans to keep up this runaway bit.
Regardless of motives, the safety of the minor is always the priority especially in a situation where they live apart from family with a stranger.
Gotou raised my respect for her with this chapter.