Some locations won't even allow you to bring WAG bags, even if you've got a reusable container. The worry is that you'll get to the takeout, and dump the wag bags into the dumpster, which then goes into the local landfill which may or may not be approved for human waste. Many different things (including paint cans, food jars, etc) may be allowed, depending on the ranger you get, but the PVC tubes are pretty well universally accepted- perhaps because of bigwallers in Yosemite, Zion, etc paving the way with the NPS.
I would avoid used polyethylene food containers, because I've seen how easily the lids (on most of them) break. Working in a deli, we went through tons of these things, and while the jars themselves are awesome, the lids are brittle.
I would also avoid WAG bags unless you put them inside another container- I've seen these things get poked and tear open on the river- definitely not easier to deal with when that happens.
Paint can sounds like a good idea. Do you just use a rock to reseal it? Does this cause denting, and thus, a loss structural integrity?
I'd stick with the PVC tube. Poop on a double layer of paper towel, fold up your present, and put it in the tube. At the end of the trip, empty the whole thing right out into the pit toilets. Our latest one was 4" PVC, ~16" long, and served 2 for a 6 day trip with room to spare.