IMHO this is very good already - I'd keep the sub as is and wouldn't touch it anymore for now.I really don't know what causes it but without the sub tuning with non-boost is impossible again. Below is a measurement with a slightly lower frequency on the sub.
The dip around 100Hz is IMO most likely caused by SBIR from the glass sliding door.
My suggestion would be to push the speakers back, closer to the glass. That should push the dip a bit higher in frequency, and might make it less deep.
EDIT: By the way, how far exactly is each speaker from its adjoining side wall at the moment?
Then re-run RoomFit, but adjust RoomFit correction frequency range to 20Hz-200Hz.