Wouldn’t she come to the door and maybe call out if she wants to be let in again? Or it could be just curiosity about what was inside. One of the strays I fed, would step into the house and look around a bit, but as soon I stepped out would follow me.
Years ago I bought four cheap plastic coolers and cut cat-size holes on two sides, then put an old blanket inside. Placed them around the outside of the house and yard. I don’t know if any of the feral cats around used them, but the local possum community was quite fond of them.
I wonder whether she was crying because she was inside, or crying because she’d been shut up on her own? She may have expected that “inside” would mean in the immediate presence of you and/or your other cats. And as she’s presumably grown up among members of her cat colony she may never have been alone before.
I agree that you needed to isolate her – you don’t want to risk immediate cat fights, or spreading fleas all over the house. But it might not have been being inside that she was crying about.
I sent you a PM.
I’ve been watching each night to see if she is on the porch but she has been disappearing after dinner. I don’t know why I had a feeling she would be around that first night. And she didn’t cry to come in. She just sat in front of the door. So now I look out every 30 minutes or so to see if she is out there.
I imagine being shut up alone in a 12X12 room was pretty frightening for her. She actually did ok the first night but she was probably getting panicked by the second night that she would never get out. She’s totally back to normal outside now. Hopefully, if I have to bring her in again, she won’t be as afraid. She’s not around again tonight and the temps are going to be just above freezing so I’m not too worried.
I’m keeping the room closed for the foreseeable future. I sprayed for fleas and hope any were confined to the room. And she seems healthy but I can’t be sure of that so I don’t want my cats in there right now. Anyway, that leaves it available as the kitty hotel. 
Spray/bomb and vacuum the room every few days as flea eggs can remain dormant for a long time. When we moved our dogs outside, my brother had to vacuum every day for weeks before the fleas were gone. While the dogs (the last two of four were moved outside) were in the house, we’d rarely see any fleas except on them. Once they were gone, the fleas would quickly jump on us.
Dupe
Hey, don’t judge. They might have started out like you, harboring a stray.
We’ve had very good luck with Frontline, although it took a month and two applications to begin working.
One of my sisters got a third cat in a similar manner. The hoarders across the street never noticed the poor thing had been missing until she asked if they wanted her back.
She never really got an answer.