Is this really the trend? If so, how does LimeLM fit in here?
I wouldn't call it a trend.
I acknowledge the fact that allowing that floating server to activate on a VM is potentially dangerous, in that the user could theoretically clone the VM itself and then sell it to others (this is the case for TurboFloatServer, correct?).
It's not the problem of them selling it to others, it's a problem of them running multiple VM instances at the same time. Each VM instance would have its own TFS instance that can server license leases. (By the way, this problem is the same for every single floating license server product on the market).
How do you recommend I approach this?
You could allow them to run the TurboFloat Server on a VM, if you want. It will be hard (but not impossible) for them to clone the VM instance successfully.
It's up to you.
If we did allow them to install the TurboFloatServer on a VM, is there a potential for problems with the virtual machine changing its "fingerprint" during the virtual machine's normal operation?
Yes, that's another potential problem. It depends on the hardware they're running on and how the VMs are configured.
All of these are reasons why we recommend only running the TurboFloat Server on real hardware (it doesn't have to be on expensive hardware -- cheap and small works fine). Your app, using TurboFloat library, can then run on anything (VM instances, real hardware, etc.).