You can lock the interface with ctrl-g and then all keys pass through.
The idea was that users should spend most of their time in "normal" mode, deferring to "locked" mode only for cases like you mentioned (ctrl-r in bash or in vim). The modal ergonomics are built on that.
I'd ideally like to find one word that describes locked mode better than "locked", which I agree is not ideal. I spent quite some time thinking about it and asking others, but most of us are not native English speakers - so maybe there's something obvious we're missing. :)