That is an expensive option: twice thr connectors, twice the controllers, installation time, more to go wrong. One upgradable battery is simpler, and the cost of the 'extra' batteries may not be that much.
Doesn't have to be. The controller will then be in the car, but yes, twice (or more) the connectors, and a bit more installation time. But look at the unveiling event. When Elon start to talk about the Model 3 you see the battery. 4 rows of two modules for a total of 8 modules. If the base battery is only the 4 in the middle then they can add two more modules to the front and two more modules to the rear to expand the battery. No shifting of the battery needed, just add 2 or 4 modules. My guess is that it is one connector in the car for each module, both for the cooling and the power, and each module could separately be replaced when needed. Or maybe two and two are linked together.
In the next generation of Model S/X I guess they will reuse this modules system, but it will get 10 or maybe 12 modules and each module will be about 12-15kWh - or more with later upgraded chemistry.
... OR: each module in the base battery of the Model 3 will be about 7kWh for a total of 56kWh (55), and the biggest battery will have 8 modules of 11kWh for a total of 88kWh (90). And then there is a middle battery option of 4*7+4*11=68kWh (70).