I've noticed the same issue.
I'm hoping someone from Mikrotik will take a look at this thread and comment...
The behaviour is exactly the same as with Net-SNMP on generic Linux.
It was introduced I think in version 5.5, and I therefore assume that RouterOS uses a port of that version.
At the time, it was changed to allow broadcast SNMP support, but an unintended consequence was that it broke multi-homed installations.
It seems that the fix is in Net-SNMP version 5.7.
Perhaps Mikrotik can look into integrating this into RouterOS?
- Multi-homed agents send UDP responses from the proper IP address