Just cheaper, and a bit easier to handle on the BoM since it can be used for other interfaces too (ie you can have two TXS0108 chips to do all your level conversion, instead of one MAX13035E and one TXS0108). It's also easier to get (no stock on the MAX13035E at Digikey) and easier to solder.
With the clock line, your description is correct. The idea is to compensate for delays caused by the level shifter, since those would mean that data received by the master is not in sync with the clock signal that was originally sent out. Since the feedback signal has gone through the level shifter in the same direction as the data, it will be in sync.
Regarding the SWD on the Edison: nice work! I'm planning to just hook up a UART and a couple of GPIO pins so I can use the embedded bootloader to load code. Not as flexible (can't debug with that method) but it should be adequate.