Hello,
Foreword: I think we all agree, that certificate based authentication can increase security. I'm just trying to figure out, how you would like to handle things at scale (thousands of machines and more) and what you think about different options from a usability perspective.
I don't follow on this question.
And Veeam does not do "
security by obscurity"

. If an attacker takes over the backup server while still having the option to run scripts with admin permissions, then having certificate based authentication is not really helping against anything.
The attack vector is that a compromise of the VBR server is an automatic compromise of every single connected agent.
That's why one should protect the backup server. There are many Windows hardening guides by different organizations (DISA STIG, CIS Benchmarks, whatever) and one can also follow the
Veeam best practices guide
An additional attack vector is that if an attacker somehow gets limited privileges on one of the backed-up virtual machines, if an attack is successful against the local SAM to figure out the local admin password that Veeam uses to perform backup jobs, that also means an automatic compromise of every single connected agent.
as far as I remember, that's a low risk with NTLMv2 and proper passwords. But agree in general, that's an agent-specific attack vector if same credentials are used everywhere.
About pre-installed agents: yes, these agents behave different (scheduler is running on the agent side instead of the backup server, no manual "start / stop" of jobs). Whether it's really a "limitation" or just "different" is something each customer needs to decide on its own. I'm just saying, that there is an option today available, that does not require storing passwords on the backup server. For AIX & Solaris, we only have "pre-installed" agents and customers definitely use it.
but we totally lost control over our backups, which is unacceptable
could you maybe describe what that means? what exactly was lost?
Best regards,
Hannes