I don't think the OP is asking about using a water bottle for a storage container but rather a cage with a tool box attached.
You mean like the Topeak Ninja multitool cages, or the Specialized Zee cage or EMT, Synchros Matchbox, Lezyne Flow, Tallac Designs Tool Pouch, etc?
No, by the description of screwing the lid on, I think the OP is asking about the numerous tool keg style containers that mimic the shape of a water bottle to fit in the cage.
Me, I decided to forgo the water bottle cage and am using a WolfTooth B-RAD Roll-Top Bag with the optional mounting plate. It fits the cage bolts under my downtube.
I chose it because, though it's not strictly waterproof, it was probably good enough. Because it's soft sided, it's not going to rattle, and at 1 liter capacity, it could hold more. Fitting a 29" tube in the tool kegs doesn't leave much room for anything else. I guess that's how not to have rattles too. And ithe WolfTooth is wide enough I can squeeze my hand in and reach all the way to the bottom. I'm not going to be able to do that with anything rigid that's the diameter of a water bottle.:
In addition to the tube, I've got a <goes out to garage and checks> CO2 inflator and two spare cartridges, multitool, chain tool, chain link pliers, quick patch, and tire levers. And there's still more room. Actually, it's a gravelish tube, say 700x32c, but a 29x2.3 would fit instead.
I did need to space the mount farther away from my downtube for a couple of reasons. First, the underside of the mount has ribs that would have dug into my frame, and second, I wanted it farther from mywith exposed shifter cables. I think WolfTooth has B-RAD fittings that would work, but I made my own spacers since I was too cheap to buy some and too impatient to wait for shipping.
There are other similar pouches that also don't really need the bottle bosses and can strap directly to a frame tube, but I chose the WolfTooth because it did have a mounting plate, so I could be sure it wouldn't slip towards my chainrings and the strap wouldn't dig dirt into the paint.