I am no electrical engineer either. The way I understood it (except from seeing magic smoke being released from a ESCs BEC right after pluging in the lipo) is that BECs, like everything else, have their tolerances. So even two identical BECs will not have the same voltage output. Then there are two types of BECs, linear and switching. Mixing the two types is bad, but even two (or more) BECs of the same type may result in failure. That is because the BEC with the lower voltage output essentially becomes a load, being supplied by the BEC with the higher voltage. Due to the low internal resistance of the BEC circuit, the current flow can become high enough to destroy the BEC with the lower voltage. This is even worse for switching BECs, because they work by switching the supply voltage on and off really fast to create a resulting lower voltage. Two of them will never be in sync, so one BECs switches off, the other on and the voltage will be fed to the switched off BEC. Perhaps there is an electrical engineer around, who can explain it better (or correct me ).
The capacitor is just a passive element. It is charged by the BEC until it is full. If the RPi draws more current than the power module can handle, the voltage of the PM will drop below the voltage of the capacitor and the capacitor will discharge, this eases the load on the PM and the voltage will rise again. This will happen really fast of course and the voltage will stabilize at some value, as long as the power draw of the RPi stays constant.
Two batteries in parallel of the same voltage are no problem either. If one battery has a slightly higher/lower voltage, they will level out quickly. If you connect a charged and a discharged battery interesting things will happen, especially with lipos.