Controls should be entered and exited as fast as possible. It is very, very easy to "save" several hours at controls that can be better used for sleep. Having spare footwear goes against my philosophy of wasting no time at controls or maybe it is best to say being very mindful of how much time I spend at controls and to do so with reason. I see little/no benefit to flip/flops against a huge time cost. On the other hand if I am not well, I stop and fix whatever is not right but when the cranks are turning well, it is best to get the warm muscle back on the road ASAP. Then to use that time for a sitdown meal or sleep. This is just my opinion but it works for me.
One of my metrics is having my fully geared up bike with 2 filled water bottles to weigh less than 28 pounds. So, not much in the way of spare anything but I am going to cheat and use a drop bag at Loudeac.