3) What do these stacking plates do? Connect drives together? I cannot seem to find them.
Yes. The NCase M1 uses them, see here:
NCase M1 Accessories
4) It will not be possible to achieve tool-less side panels on this model. On a different and more expensive one, yes. Dust filters could be added sooner but I will need more time to work on that.
Ok, I see. I guess I could use M3 thumbscrews, 2 on each panel placed diagonally for as hassle-free panel disassembly as possible. There's also magnetic tape but that stuff tends to be thick.
For dust filters, I think you'd need something permanently glued to the panels or maybe very fine metal mesh. I think for a case this small, cleaning is much easier and cooling is limited, so filters are not very practical, but it would be nice to have the option.