We had exactly the same situation - no SME backups were possible since the security patch was installed.
Deinstallation of KB5001779 was possible (Exchange 2016 CU20) AND a solution for this issue: SME backups now are running fine again!
Of course running Exchange without this security patch is risky and thereford not a good solution - but running without backup is not aceptable at all.
We will migrate to SnapCenter as soon as possible.