Your inference may also be incorrect. I don’t think you state where you VPN connected to, but I assume somewhere outside your geographic region. What it may have done is connect you to the MSFS content servers in the region where you pop back out on the public Internet i.e. you are not connecting to the same servers as you were without the VPN.
It could be content throttling, but they would have to do this on an IP per IP basis as I assume the connections are over HTTPS, so unless they are doing HTTPS packet inspection then they still don’t know what your traffic is, only the IP, and service port(s).