It was a suggested possible reason for what you were experiencing and if you are now happy that this isn't the case, then i guess we are back at square 1 again.
The framerates you are getting do not sound unusual, compared to what i get and what others have reported and it is odd that the elements of the PC that you might expect to be causing the bottleneck are not at all stressed. I have just had a look at MSI Afterburner, whilst playing XPlane 11 via FI XP and seem to be getting similar results, but i am afraid that i don't know why.
Could it be that memory is getting filled up and is having to be swapped out to disk constantly? Given the size of memory that modern day PCs have and the fact that my memory usage never gets much above 50% of my 16GB max, it doesn't look like it.
Could it be that some of the code is written so that it sits and does nothing for large parts of its cycle? I'd expect that to be picked up pretty quickly during the optimisation process, so again, probably not.
Maybe, along similar lines, FI and XP11 have to wait for each other to stay in sync? Have you tried running XP11 without FlyInside, to see if the symptoms are the same?
Could it be that short spikes in CPU/GPU usage are being missed by the monitoring software, possibly because XP/FI/OH software is using all of the CPU power?
Maybe not, but something has to be causing the bottleneck.
I'm sorry that i don't have the definitive answer, but i hope that someone else in the community might have identified the issue, although given the relatively low reported FPS readings, i suspect that any solution bringing significant increases would be shouted from the rooftops.