Although Nexus Mod Manager had a toggle archiveInvalidation option, but I've no idea what it did.
Presumably the "load loose files" check box does it for us - although no matter how many times I check it, when I open the window again it's not checked

I'm not sure what the "load loose files" option does
per se, but it's not intended to be used all the time. It's something that you enable for a single session for... some reason or another.
I've never touched it, nor have I touched NMM's archiveinvalidation utility, and I've had no problems at all with texture replacers.