Pergunta antiga, mas eu estava apenas olhando para isso e pensei em responder.
Há uma boa discussão aqui: link
Mas, basicamente, a resposta chave para a sua pergunta é que tudo bem e a VM ainda vai sincronizar via Hyper-V durante a inicialização, mas o próprio Windows usará o servidor NTP que você configurou.
... you can “partially disable” Hyper-V time synchronization. The reason why I say “partially disable” is that you do not want to turn off the aspects of Hyper-V time synchronization that fix the time after a virtual machine has booted for the first time, or after the virtual machine comes back from a saved state. No other time synchronization source can address these scenarios elegantly.
Luckily – there is a way to leave this functionality intact but still ensure that the day to day time synchronization is conducted by an external time source. The key thing trick here is that it is possible to disable the Hyper-V time synchronization provider in the Windows time synchronization infrastructure – while still leaving the service running and enabled under Hyper-V.
To do this you will need to log into the virtual machine, open an administrative command prompt and run the following commands:
reg add HKLM\SYSTEM\CurrentControlSet\Services\W32Time\TimeProviders\VMICTimeProvider /v Enabled /t reg_dword /d 0
This command stops W32Time from using the Hyper-V time synchronization integration service for moment-to-moment synchronization. Remember from earlier in this post that we do not go through the Windows time synchronization infrastructure to correct the time in the event of virtual machine boot / restore from saved state or snapshot. So those operations are unaffected.