I always felt like MMO runs on a very soft sort of canon, and some things happened more than other things happened, even with regards to things that happen in the main collections.
So sometimes something happens that blows past the norm of awfulness for the series, but doesn't seem to stick or ever get referenced again. It happens in its own story, but not necessarily in subsequent ones.
A good example is Jones camming one of his kids. It blows past the norm even for the series, and some the characters don't react to it even as much as you'd expect these people to.
And then all subsequent comics are as though it never happened. In bad gateway they're horrified and it becomes a significant plot point when it turns out he's keeping his infant daughter in a cage, which is much less bad than the previous incident. The cage incident, as part of the long-term narrative that's become more central to the series with each collection, happened to a far greater extent then the Camming comic happened.
So if you pick the worst things we ever see Jones do he's a lot more irredeemable than if you try and take into account the degree to which different incidents stick, what the current Jones you see on the page is really likely to have done.
Stories like Felt Hats and Jones injecting his eye with rotten orange juice are, I feel, a good bench mark for what Jones is usually like, rather than someone seriously and regularly sexually abusing both his sons.