In my experience, even when the crew is ranked Elite they're not great with Shield Cells. They kinda waste them. They're damn good with fixed weapons, and can pull off the FA-off moves ya see other Elite NPCs do, they also cheat with rail guns like other NPCs, but they're not super smart with anything heat related and they waste cells.
I am PRETTY sure they still earn the same amount of rank if they're flying the mothership and you split the rank gains the same as if they were in the SLF, since I did that plenty as I ranked mine up, but I can't say for 100% certain.
An Elite crew member is pretty cool though! They can practically clean out a CZ on their own.
EDIT: They do still use chaff and other tools like that, but they just don't use them as intelligently as a human (which prolly won't surprise you). I don't always use a lotta chaff so I can't tell ya how good they are with it, or if they just shoot them off as quick as they can or time it perfectly.