As for Lightning; it is genius, it bypasses any update time, I assume you just won't be able to close/open a pay stream during the downtime of BTC (which is already really low).

I'm pretty sure that's how it would work, yeah. Also, there are at least two major lightning implementations that I know of (CLI and LND), so that helps to even out any bigger failures within lightning itself when it's not the same software with everyone.