Each case is slightly different and getting the answers involves trawling through ASM and WDM.
So do you mean that (e.g) the LP fuel valve is not opened/closed by ECU/EIU but direcly by the switch? EIU/ECU just knows the position of the switch/valve? Correct, LP valve opens or closes depending on the master switch position (and associated fire switch), in fact the EIU "knows" only the switch position not the valve position.
But what about the engine selector to START/IGN? It will open 1 PFCV. It direcly opens it? It doesn't transit threw the EIU which sends a signal to the pack controller? EIU, again, just knows the position of PFCV? A start command is sent from the EIU which controls a relay to close BOTH pack FCSOV.
So when does the second PFCV close (of course, the pilot has pushed the master switch)?
Isn't it the pack controller? See above.