My different kits have a lot of redundancy between them, for this very reason. Each is designed to do what it can do in the space I have for it. Being a guy who goes to work in a suit and tie each day, my EDC stuff is all in a gallon sized zip-lock, that goes into another bag. Anymore than the gallon, and it becomes too much to lug with me on the subway.

I've thought that maybe I could not repeat things that are in my EDC, but most of the items I repeat are not that expensive and some are tough to buy except in sizes that require me to use only a few in each kit. I bought nitrile gloves in a box of 50, some went into each of the various kits. Same with for example garbage bags, a useful item, but how bad is it to have one or a few in each kit, and how expensive is it?

As far as being able to use your bags as planned, I see nothing wrong with that, but I'd look at each on their own and think about the combinations you would use.