Let us craft from Retainer Inventory

[Flyojumper]

/snip.
Of course, if the solution to the new "problem" is far from self-evident, then it makes the player have to think more than he would have otherwise done; i.e. opposite of dumbing down.

You are overemphasizing and overestimating the strategic elements added by micro managing item transfers between retainer and main inventory. It's really nowhere near as strategic as you make it sound. I'm curious, would you be a proponent of say reducing the main inventory space to 10 slots? After all, you could argue that it forces players to think more about what they are going to use those 10 slots for. There are ways of making a system more strategic/engaging without making it cumbersome and tedious to the player.
Also, you have not touched on the fact that removing a less strategic forced step would increase the overall time you spent on the strategic part of crafting.