Howdy Belter,
Good questions. Let's see if I can't make this clear as mud, how 'bout?
1. Shuttle's a convenience item, Belter. That 5-load cargo bay in the shuttle is in addition to you main scrapper's bay, but they are indeed separate. You'll sort the prizes when you get back to station, but on the job? 5 in the shuttle and however much your bird carries in two neat stacks.
2. I'd say that, as a canny and practiced Belter, you've probably got the same ability to pull parts and have Bits waiting for you in a Shuttle. Preparation is key, right? Anything you can do in your main Airlock's is meant to be accessible through the Shuttle. Shuttle is, essentially, another Airlock with all of the drawbacks and advantages that entails. It's how the two-person salvage operations manage to operate, and it'd proper suck to be the partner gasping while the other's camped out next to the recharge port. Chalk it up to being fair and equitable in a Belt that...well, ain't.
Hope that helps.
Chariot, out.