I resolved my MSFS freeze issues by changing a setting that has plagued Windows for many years: power management of ports.
To reduce energy consumption, Windows has a default configuration of turning off ports that it perceives as being idle. At best, you will experience a lag while the affected port is re-activated (e.g. you moved your mouse), or you may need to unplug/plug your peripheral device, or the port may not come alive at all (the source of complaints about dead ports). This power scheme made sense years ago, when it was important to squeeze out every watt. With today’s machines, not so much.
This issue can affect both USB and BT ports, which is why troubleshooting often seems to have random results. It’s not the type of port, per se. Rather, it’s how effective individual devices are at re-energizing sleeping ports. And meanwhile, MSFS pauses while it’s waiting for the device input while the port is waking up (or not).
Here is how I resolved my freezes:
Device Manager > Human Interface Devices > BlueTooth HID Device > Power Management Tab > Uncheck 'Allow the computer to turn off this device to save power"
Device Manager > Universal Serial Bus controllers > Intel® USB 3.1 … > Power Management Tab > Uncheck 'Allow the computer to turn off this device to save power"
. . . and repeat for everything in Device Manager that appears to be relevant.
Note that you will not be changing how the ports function, nor how they are configured. You will simply be telling Windows to refrain from killing the power to those ports when you haven’t moved your mouse or controls for a while.
I have not experienced any freezes since I changed these settings.