Native speaker. Wow! This is not an easy sentence for anyone, but after reading through it several times and getting confused a bit I think "which" actually refers to the actions of others. From this context, we don't really know what those actions are, but they are described as what "others do largely by protension". *Those* actions (the "which" actions) come from their second nature.
Do you know the phrase - "take that with a grain of salt"? In this instance, that means that I am providing a guess, but someone might have a better answer...