I've got the itch to set BKChem up such that it satisfies these conditions imposed by Wikipedia on chemical structure drawing and I am using Ubuntu, but I don't know where my question would be best posed. Is there another StackExchange where I should ask this question or will Ask Ubuntu suffice?
Yeah, it should be on-topic here.
There may be a more appropriate site (is there one for BKChem and/or Wikipedia?) but failing that, Ask Ubuntu or Super User are fine alternatives.
Just reread what's going on. Given this is isn't just about using an application that existing in Ubuntu, it's about the platform-specific configuration locations, this is definitely on topic.