Would it be possible to add a configuration option to allow pets, such as the Golem created from the Golem Kit or the Bat from that one bat armor, to take direct damage from the owner (sword, bow, etc. but not flint and steel)?

This zero-damage behavior appears to not be limited to pets created by this mod. I tested a Forge 36.2.0 server with just Dungeons Gear 1.16.5 - 3.0.17 installed and connected to it with a client with the same mod version installed. I tamed a horse and attempted to kill it with a sword, but it took no damage. For comparison, I /summon a new horse, and without taming it, was able to kill it with a sword.
I did the same with an Iron Golem spawned from the Golem Kit and it didn't die, while another /summon Iron Golem was able to be killed.

I saw #86 but it doesn't seem to describe the same issue here. I did not find anything in the config that addresses the current issue.

The motivation for this change is that I found that another mod, Project MMO, is counting up experience points in Combat levels even when the mob is not taking damage due to this mod. This can be easily exploited by hitting your pet endlessly and racking up experience extremely quickly.

Config option exists in latest beta