You are right in that sometimes the update process can cause problems.
Also Parrot cannot be updated with the Qubes Updater - this is an
upstream bug that I have fixed, but has not yet filtered down to Qubes.
I outline a process for avoiding conflicts here
In Debian you can use apt-mark hold to ensure that packages are not
updated or removed.
Since you are using separate templates for the pentesting there is not
issue conflicting with other standard templates.
I never presume to speak for the Qubes team.
When I comment in the Forum or in the mailing lists I speak for myself.