Yes, this is a special situation with no real good options because paypal is behaving like its usual dickish self. I still don't think that it harms paypal or helps anyone to mark their email as spam. Best would be to create a rule to drop their incoming messages.
Or use GDPR or some other legal option if you have time to spare and want to cost them some time=money in dealing with your request.
Training a spam filter is not the same as creating a do-not-deliver rule for a given sender. Unless you manage to convince the filter that paypal is the same as a viagra scammer (good luck with that), you'd still get those messages from paypal.
Maybe some providers also denylist the sender-receiver pair when you click spam to combat this problem nowadays; back when I used public email services this was rarely the case. Nowadays I use a different system altogether so I don't know if this might now be common.
Either way, this is not what the spam button is for, but from this subthread I see that enough people on HN already don't understand how these systems work (and education is hard: people don't even read relevant oneliners pushed in their face at a relevant time, such as error messages), so I guess there's no hope for the general public altogether. I didn't know this is an entirely lost cause and is making me rethink about reporting spam on platforms like reddit. I guess they get so many false positives that I'm wasting my time reporting anything as spam ever.
Most of my email is on my own server, but in my experience (with gmail, etc.) marking a sender as spam will keep them out of my inbox going forward. I would personally filter the email, but for those who don't understand that process, marking as spam can be effective as well.
I see your overall argument, however this dilemma is ultimately caused by PayPal's ruthless/unpredictable ban policy