Well, as mentioned earlier in another thread by some of us, probably the best choice would be making something akin to bags of holding that give you a few bonus inventory slots each, with them being impossible to find and players getting one such bag for every "crafting" skill they chose. That way those with two or three crafting skills would still have a free row in their inventories or so... Optimally, every one of these bags could have a list of items that are allowed inside (so that we wouldn't be able to abuse them, and even runecrafting could get its own rune pouch), but it's not necessary, really.
How about a simplified approach? If you take smithing you get a Bag of Ingot Holding. It holds every ingot you find and nothing else. If you take Tinkering, it holds all the tinkering component items like Brass Mechanisms and Voltaic Cells and such. *Edit* You edited yours while I was writing this. So you pretty much covered this with the idea of the runecrafting bag.
Well, the approach is simplified for us, but for the creators that would me more work, because, while they have the code for containers somewhere (the old crafting tools used it), there's no code for disallowing containers to hold certain items, or only allowing listed items, so they'd have to write that one from scratch. And while I am sure that they are capable of writing that, I don't want Nicholas to die from overworking himself.
I am not convinced that it would be less work. Here is why: The old containers lost the contents when you saved and reloaded. The same containers would suffer the same problem. It would require a rewrite either way to get something that works. So we may as well ask for what seems the best solution from the start.
I'm all for the idea of an additional bag for anyone who has a crafting skill. The bag could gain a couple of slots per natural skill in each of the crafting stats that the player has. I'd say that it would be a good idea to have this bag set to only carry crafting reagents, and nothing more.
How about simplifying it and just giving people with craft skills a couple of extra lines of inventory per craft skill. It's not like there's no more room in the inventory window... (and give us the tools to add it in mods as well so half-craft skills like rogue scientist, clockwork knight etc can get one extra line perhaps).