I just confirmed in creative that I can pull waste from a chest and distribute it using item ducts and it places one item per slot in the short term waste containers. I don't see it stacking.
That said, I'm not sure why my survival waste container blew up. The arctic ambient is -20C, and they are submerged near bedrock. I may pad my containers with cobble so they can't be more than half full.
Much to my surprise and dismay, my little 6 core reactor blew up in survival when I logged into the server.
I must say everything that works great in single player has consistently bombed (pun intended) serverside. I think it happens on chunk load or unload during initialization because I was standing in that room when I logged out. This was the first time I tried to let it run across sessions. My PBR has never had a problem, but I never run it except in supervised short bursts, never always on.
Yes, I know I run MCPC so I can't really ask for support but i"m climbing the walls because now not only is waste overreacting but a tiny 300MW 6 core cool reactor doesn't work either. Pardon my rant.