We're saying not to mess with those lists as we've seen people face some issues with them in the last few days + other technical stuff I can't speak on as that is a Xander question.
By lists we mean all three of those lists you mentioned
I've heard from others that notifications aren't exactly working properly even when added back to those lists but I'm not sure. Custom lists should be safe to add to but make sure each entry is properly recorded as sometimes information isn't updated to the server properly. I've heard of some people adding works they want to get notifications for to these custom lists in case. (I never really used these I don't know if it notifies you.) Otherwise, iirc sites like mangaupdates notifies.
I'll talk to Xander and see what he thinks the situation is like right now though.
FAQ in case:
https://www.mangago.me/home/mangatopic/21255174/
Heres some info on getting notifs I just asked
you can get notified without putting it to the lists. you click "subscribe" to it after you mark it or rate it. you don't have to add it to your lists to get updates on it. i figured that out by having to unsubscribe to things i rated and didn't want them notifying me and they weren't added to my lists

When they say don’t update your lists because the devs are working on it, does that include “Now Reading”, “Already Read”, and “Want to Read”?
I keep on seeing people saying not to tamper with lists and also mentioning nr & wtr in the same breath. Are notifs obsolete until this is fixed then?