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I had a deeper look into Net-SNMP source (v 5.4.1): apparently there isn't a sane way to fix this, other than backing up the whole settings in the default store, resetting all the boolean values, do the call and then restoring the previous settings.

It seems that Net-SNMP stores its settings (including things like the SNMP community and SNMPv3 parameters, which could logically be thought as belonging to a specific session) in a handful of static arrays, which is basically the same as having a bunch of global variables, so backing up and restoring the settings between calls (even for "get", "getnext", "walk", etc.) is probably required to allow for indipendent sessions

In other words, creating a new SNMP session with different settings from the previously opened ones currently results in the old sessions using the new settings.