You have identified my own issues with it as well.
The general concept was to have a mod that increased the usability of leather to the point that it could compete with metal, and that the ingredients on the way would 'cost' more and in time and materials in order to make them. This pretty greatly increases the cost of a full set of runic leather, in both resources, and time. Once I set it up, I had no idea how to really break down the process well enough to make logical sense.
One would assume that, before boiling, the dwarves would remove the padding on the leather, but then why pad and stud it at all in the first place? Should this stripping return cloth back to the player? These are questions I wanted to avoid, and settled on a straightforward system, with a shaky footing in logic. I would love to change the process in an update, but I haven't been struck with the golden idea of how to fix it just yet. I thought of making the entire system based on the leather being enchanted in various ways up the chain, but thought this was more of a cop out.
In regards to the bone/hoof studs, Yes! I thought this was an important way to add some additional value instead of just making them into crafts. I intended for shells to be in there, I must have forgotten about them! I'll have to add that to the next version too. Sadly, the material of the stud is lost during the creation of the armor. Your pond turtle shell studded armor would most likely be *Chicken Studded Leather*. If you can think of a way around this, let me know! Excessively long item names be damned...
Lastly, I don't think you should feel bad at all with producing a mod with similar outcome. I decided to make this because I loved playing Dwarf Fortress, and I wanted to learn how. If you trace back on this mod, and my first mod the Block Crafter's Workshop (see links below), you will see a long history of me asking silly questions while I learned. While digging through lots of other people's mods (Old Genesis, New Genesis, Masterwork, Kobold Fortress, and Modest Mod) I found lots of code that seemed related. This isn't a bad thing! Each mod provides an experience unique to the sum of its changes, and sharing/borrowing/outright stealing of code is a good way to learn.
I'm sure that if you look hard enough, you will see where I borrowed some reactions from Meph to facilitate the upgrade of leather. I encourage you to release your own version!
If you like, I am also willing to work together on a new version together, or you can use my code to expand to your own system. I'm in it for the fun and knowledge, and you aren't going to bother me one bit by putting out a mod that shares an idea.