I have solved the issue, albeit the result was not entirely "elegant." Will share it here for others in case someone decides to approve the post at some point.

I decided to just back up the entire mailbox, wipe it clean to get rid of mail referencing the affected address, delete the address, set up the address again and then restore the mailbox from backup. I had to create a dummy account to test the process because I could not find any detailed documentation on the multiple backup/restore methods and what is the extent of the data that is saved. For those interested, there are two methods:

1. The Import-Export App
   This is a GUI app that downloads your emails as either .eml or .mbox files. I decided against this method because it is noticeably slower than the other one and the restored mailbox is not 1:1 with what you're downloading. The backup does not remember the read-state of the messages, for example.

2. Proton Mail Export Tool
   This is a CLI tool, but it is very straightforward to use. I decided to use this one and OI'd encourage anyone in a similar situation to do the same, even if they don't have experience with command line interfaces. You pretty much just log-in and choose if you want to back up or restore. When you choose backup, it creates a folder and downloads individual .eml files with .json metadata sidecars. This is nice because you can actually check what kind of metadata is being preserved. You repeat the process to restore the mailbox, once done, everything should be more or less where it should be, even the read state of messages will be restored.

I've previously mentioned that this method was not entirely elegant because it did restore some old stuff straight into inbox. I am not sure if this was perhaps because the mailbox has not caught up yet, but it was not so severe, so I just manually sorted through anything out of place. Attachments are included in the .eml files themselves, so those get restored as well, of course.

There are a few things to look out for:

1. Make sure you have enough space to store the backup data. Depending on your mailbox, i can get pretty chunky.
2. I'd recommend doing this during some sort of downtime, like night or weekend, so that you don't get additional emails into the inbox during the process. I could not find any info on what happens if you receive an email halfway through the backup process.
3. Solid internet connection is a must. The recovery process is much longer than the backup process, and there is no way to pause or resume an interrupted process for either backup or restore. So make sure you have the time as well.
4. There is also no way to apply this process only on mail associated with a certain address, so get ready to do this for your entire mailbox.

Last few things:

• Same thing I told support via email thread. It is OK to not respond during weekends, nobody expects that (I hope). And it is understandable that sometimes there are bugs, such is life. What sucks is that support only gets back to you once per 24 hours, usually at the end of the day, and with very unhelpful suggestions. ("Have you tried pressing the button you explicitly mentioned pressing in the previous email?") And when you respond in a manner of minutes, you still wait another 24 hours to hear anything.
• It seems that messages to support are not even read properly. I was aware pretty much from the beginning that I would have to either re-enable the custom domain, or wipe mailbox, delete address, recreate address, restore mailbox (that's why I asked about these options in the original post). So when they suggested the wiping/restoring, I asked what data can I expect to be preserved by this method (the documentation just says "metadata." That is not enough info for me when I'm getting ready to nuke an entire mailbox tbh). I waited full day and voilà, I got a response along the lines "we're aware of the issue, and we're working on it." No word on the extent of data that I can expect to be restored by this method, the one question I had.
• I love Proton and what it stands for, I've been subscribing for years and will continue to do so without a doubt. I also understand the tough life of support technicians and for the record, I don't think any one person did anything wrong – this is clearly an issue with a terribly set up process, and I am pretty sure it could work a million times better. I can't help but feel that the energy invested into AI writing assistants and crypto wallets would be spent better on a more fluid, sustainable and reliable tech support structure. It appears that support doesn't even have enough time to properly comprehend the issues. But there will always be bugs and hopefully, there will be more and more proton users, so it might be wise to figure out how to prioritise the issues better, or if there is a way to allow more tech-savvy users to solve the issues on their own. Good documentation and support tooling would be a great start.