It hasn't been that long but I thought I would give an update. I updated my sysnand to 7.0.0 through OFW, and I also have NOT enabled AutoRCM. The consensus is that Nintendo is able to detect changes to boot0. I have an SD card for offline/CFW which has my emunand, and an SD card for online...
Sorry, it's kind of a long story but I just wanted to type it all out. Spoiler tags for neatness, with a question or two after.
So I have some questions still though. Right now I don't even have AutoRCM installed anymore and haven't booted CFW again since I restored my virgin NAND backup, and...