Technically, the game works in a way where you are allowed to do multiple runs of individual coins and still get all 3 coins without getting them all in the same run. So from the game perspective, it's completely allowed. But from the perspective of a 100% speedrun, it is debatable due to the '100%' aspect of it.

In my opinion, I don't think it should be too harshly moderated as doing this will cost the runner over a minute, so doing this strategy would be sacrificing time for less risk, which is quite common in speedrunning. That's just my opinion, though.