I use a small silnylon ditty bag, with a smaller ditty bag inside of it for daily use hygiene stuff.
Some of the first aid stuff I keep in a plastic bag inside that, to keep it clean. A few other tiny thin bags hold the spare parts etc.
I hadn't thought to weight the total of all the little bags, but it's certainly less than 46 grams for all the little bags. The main silnylon bag weighs about 5.5 grams. I made a smaller mesh bag that weighs 3 grams out of .9 oz/yd noseeum, if you used 0.7 oz stuff it would weigh a fraction less, the rest are plastic bags. I make the little mesh bags when I'm bored at night. That mesh is pretty easy to sew by the way, to make the edges, I just double it over itself then sew a seam down that doubled connection, seems fine.
I use a separate silnylon stake sack that goes in my pole bag, and if I were using trekking poles, it would go in a side pocket of the backpack. That weighs about 2.5 grams I think. But having it all in one place like you do is also a fine idea.
On boring evenings I'll trim a few more grams off the thing, but I think this is about as light as you can go and still be functional.
However, I'm also now aware that things are really not going to get any lighter, it's just what you like at that point, and one ounce more or less will certainly never impact any backpacking trip anyone will take, or shouldn't.
I don't worry about the weight of the individual stuff in the ditty bag, I just weigh the whole thing and then see if I have too much of something packed. It's now at about 12oz, including some poison oak remover stuff, which is 2oz. I guess I could put the stakes in there too, there's room, though I think they are little too long for it, and I like to keep them somewhere they are sort of held in place, either by tent pole or in a side pocket by water bottles etc, that way they don't do any mischief. You can attach the tent stake bag cordlock/cord in the pole bag cord lock cord so it's easy to get out when you stop to camp.
Have fun. Your thing sounds nice though, I bet it could be made for less weight with a mix of mesh and silnylon and no zipper., maybe around 20 grams I'd guess, give or take.
After looking at the pics from the site, I realized, there really are not that many solutions to the same problem when it comes to gear, that's just a slightly neater and slightly heavier solution than what I ended up doing. personally I don't like zippers on stuff, it's something I've grown to want to move away from, but that's just a taste thing. Drawcords with micro cord locks are just so easy to maintain and replace, and weigh nothing.