1. I highly oppose the idea of making the crates like workstations. Like that, you can't really carry them around. It's nice to carry a box over to the mine, fill it with ore, then carry it back. If Dasius did this, he would have to code in the movement of everything inside the crate. Also, that way you can't make flying machines, or fling boxes into the air.
2. I haven't had any problems with getting a shield through the door, though I've only made one shield. I suggest that if it's too big to fit through the door, slide it through the gap at the bottom of the window to the right.
3. I think that is a good idea, though unless you are building 3 things at once, it wouldn't really matter for you to have multiple work tables. I do really like the idea of multiple forges, but until then I suggest putting different ingots in different sections of the forge (by 'forge', I assume you mean the platform where you heat the ingots, not the thing where you smelt ore and create alloys).
4. I have also had the same sign problem. I have also noted that editing the text on the sign next to the big shop does not affect the sign by the starting shop.
5. I have not had this problem, unless you mean that when you grab a part off the table, it phases into the table. This, for me, is super easy to fix since it only requires you to hold right click, and to move it out of the table.