While I agree with you and also agree with the decision to not show it anymore, I do want to highlight this bit that you wrote:
instead dad physically abuses the misbehaving child and nothing is ever resolved
The positive thing is that it never (or so raraly that I wouldn't remember) presented the strangling as anything good or helpful. Instead it was always presented as a shortcoming of his personality. Homer is mentally ill equipped to solve conflicts with Bart non-violently. Strangling him was his only outlet and (at least to attentive viewers) it was clearly and evidently damaging Bart's development. This is for example demonstrated in a scene where Bart has such a trauma that he's getting "strangled" by thin air when he thinks his dad would go for it.
Also, with the knowledge that Bart is, to some extent, Matt Groening's self-insert, that does raise some rather unpleasant questions.
This sounds to me like you could benefit from mentally using the information hiding principle for your functions. In other words: Outside of the function, the only thing that matters is "what goes in?" and "what comes out?". The implementation details should not be important once you're working on code outside of that function.
To achieve this, maybe you could write a short comment right at the start of every function. One to two sentences detailing only the inputs/output of that function. e.g. "Accepts an image and a color and returns a mask that shows where that color is present." if you later forget what the function does, all you need to do is read that one sentence to remember. If it's too convoluted to write in one or two sentences, your function is likely trying to achieve too much at once and could (arguably "should") be split up.
Also on a different note: Don't sell your ability to "cludge something together" short. If you ever plan to do this professionally or educationally, you will sadly inevitably run into situations where you have no choice but to deliver a quick and dirty solution over a clean and well thought out one.
Edit: typos