So with the "add to new" and "remove from new" lists, is there any way to apply them to already loaded torrents without manually going through and looking for duplicates/bad trackers? I'm using https://github.com/ngosang/trackerslist  as my catch-all.

Also, would be nice to be able to have those lists auto-update with the raw text at specified sites, would remove a lot of my headaches.

Not the solution you want to hear but the most configurable: run a local retracker. Then add its IP to all of your torrents I think the agreed default was http://retracker.local/announce
I don't know what server software there is for this.

https://online-help.tixati.com/help/100/replacetrackers.html

the github list are the most recent.  i personally only use the udp, ocassionally adding new ones from the torrents.  it becomes occasional to copy/paste to a text file and manually remove duplicates, which Ultraedit, as one example can easily do.

ideally, if peer exchange is active, over a short period of time, all of the active seeds/peers will become active.  in low seed population, dht may be necessary.