I think PVE support several standard Linux/Debian packages for this and it's not managed by Proxmox. The manual suggests manually editing the default chrony configuration: https://pve.proxmox.com/pve-docs/pve-admin-guide.html#_time_synchronization . I don't expect configuration files to be overwritten by Proxmox or Debian updates. If the default configuration does change a lot (which is unlikely), the Debian upgrade process allows you to see the differences and allows you to change or combine it however you want.
One way to prefer the internal NTP servers and still not modify chrony.conf is to add a new file in /etc/chrony/sources.d directory, like internal.sources:
Code:
server x.y.z iburst prefer
server a.b.c iburst prefer
Note that this does not remove the "poking around" but ensures (I think) that the internal servers are preferred anyway.
But, as said, the package upgrade process does not overwrite chrony.conf but provides you the option to check before deciding, if you have changed it.
