It's probably something that he shouldn't say out loud, but I think this statement is true for every creator who's working on something new. Who the hell knows if this thing is going to work? When I designed Blind Forest, I was always having second-thoughts whether mixing Metroid'ish gameplay with precision-platforming mechanics would actually work. Would those two genres actually match? Would people adapt to it? I thought it was fun, so we stuck with it... but I always thought it could totally backfire. My motivation was simply to bring better platforming to this genre, cause I didn't understand that in games where platforming is one of the main components, the platforming usually felt pretty bare-bones.
As I'm writing this, I'm already working on a completely new game where we're mixing various genres together and I love it - but we have people in the team and on the publishing side that are less convinced. Such is the nature of creativity - You see some boundaries that don't make sense to you, so you try to take things a step further and the only two outcomes are that you're either batshit insane for trying what you want to try or you're actually seeing something that others aren't seeing and you might just have struck gold.
So let's just hope Kojima is onto something :)