What drawbacks to bucking, then boosting the same current?
Apart from the lost of efficiency that you have already identified, the other drawback is that the current that will flow through the 5V line will be higher than if you'd provide 12V. So it means that you may have to run thicker cables that can carry more amps (more expensive, less safe).

If you need to provide 12V at 1A to two modules, the 5V line will have to carry at least 4.8A. This becomes to be quite large. Check your wire gauge and connector specs. Moreover, this could cause a significant voltage drop if the wiring length is long. 

You said that "Most modules need 5V and low amps". So if the 5V modules actually need relatively low current (in the range of a few tens of mA), it may actually be acceptable to deliver 12V to the modules, and use a simple linear regulator for the 5V, and no buck. Overall, it may be more efficient than using boost for the 12V modules, you'll be immune to voltage drops for the 5V modules, and you'll carry less current through you whole installation. It really depends on your application, but choose wisely.

Regarding the batteries ability to provide the required current, it seems to be OK (check the discharge curves, you can find some easily on the internet). But the lifetime will be very short. After drawing 20/30 times the power to produce 12V@1A during 30s, I think you'll need to change the batteries.

Note: if you draw 2A from the alkaline batteries, their voltage is not 1.5V anymore. It will be more like 1V. Check this, as well, because 4 batteries will therefore not be enough to provide 5V. You'll need a boost converter, even for the 5V.