Trust me, a bench OS needs .NET like we need the plague.
You can make a tool to activate HPET using the command you mentioned above. One small problem though. You will use bcedit /enum to check if hardwareclock = true, right? Except it will be flagged true the moment you run the "bcdedit /set useplatformclock true" command, yet in reality it's only in effect after a reboot. Now good luck making that user-friendly AND tamper-proof.