OK, I wasn't missing anything.
As a favor for the the person giving you free labor who finds it easier to organize things that way, even if to you it seems like pointless beurocracy, we all have different organizational styles and they find it useful to make sure bugs/scopes/requirements are in Issues with the solutions in Projects?
Yeah, I think you're being unreasonably weird, and on further reflection I don't think this is even a generalizable enough problem to be worth talking about, it's just some weird idiosyncracy of yours to refuse on principle to do trivial organizational work that the maintainers of the project you'd like to contribute to have said makes it easier for them to deal with your contribution. (trivial work; you aren't even saying it would be a burden in terms of time/energy, just that it's a weird principle you have not to do anything you don't want to do even if it makes things easier on other people).
It's kind of just a true-ism of any kind of work we do collaboratively (and submitting a patch to a project that others maintain is such) that you need to do sometimes do things out of consideration for what works for the other people.
I guess I am curious why you are insisting on sending a PR that you know doesn't follow the process the maintainers have asked for -- instead of just not submitting the PR at all though? If you're worried about your time being wasted, wouldn't it be best not to submit the PR at all? Make your own fork that meets your purposes, don't interact with them at all. Now you don't risk wasting the 30 seconds it took to make the PR, when they just close it for not following their procedure since you didn't want to waste the 30 more seconds it might take to do so.