What would be the purpose of this variable in backup-my.cnf?
it is read by mariabackup that does not understand it because it was removed.

I am really not sure what these questions try to address.
I will just consider that they assume that mariabackup will not be used to backup 5.5 ; thus leaving them without answer.

Maybe you should explain why do you think it is a bug, and what is the expected behavior of --prepare if backup-my.cnf has this parameter

I don't know expected behavior, but it quite obvious that problem will happen if backup is attempted on instance with innodb_fast_checksum enabled.
I assigned this to an engineer to prioritize and investigate possible outcome.

The real problem is not the content of backup-my.cnf, but the fact that fast checksum code was removed. This apparently did not bother anyone during the upgrade, there is no mentioning of the upgrade procedure in our documentation, and I cannot find a single bug report re MariaDB upgrade and fast checksums. So overall, this feature was probably not used much and it does not make sense to implement any workarounds, but rather document the limitation .

The aim is to have expected behavior for all input configuration. I agree that you mention valid points, but not sure why you mentioned them.