Yes, both tranny leads are wired/connected/terminated together.Given the thickness of transformer wires, you may want to use something like a terminal block. Connect the tranny leads to the block (maybe using spades or similar soldered to the wires for safe, secure connection). Then wire the IEC to the terminal block (with Line and Neutral appropriately separated of course).
Not sure about the Soft Start. It has a 10A fuse, so that may be a limitation with multiple trannies. May want to ask Cristi of Connex about that.
I believe farther apart is better but I have two very close in my amp enclosure and it seems okay (there is a very low hum, though, so...).