You'll notice that I don't actually use a 3D Clear Organizer Cube as my 3-1-1 kit. I use a slightly larger, quart-sized fully transparent makeup kit I bought from Paula's Choice (although it's available elsewhere).
One big problem with the standard quart-sized Ziploc baggie is that it's not pleated. If you get their zipper-tabbed version, the bottom is actually pleated, making it easier for you to pack them with your toiletries.
I tend to spend a lot of time building a toiletry kit, to be honest. I'm always on the lookout for good little containers to decant into. And except for a couple of items, I rarely ever need 2 ounces of anything, so I can carry a lot of little 1-ounce and 1.5-ounce bottles.
Getting some of your toiletries packed in your child's 3-1-1 kit is actually a pretty smart move. Every person gets their own 3-1-1 kit, so you can easily get various things packed into everybody's 3-1-1 kits so they're all balanced.