I think they should, at check-in, show the onward boarding passes. Technically, since they're not flying in F, they may not have free bags (unless the award is ticketed in full-fare Y).

But they should be able to use the Elite check-in due to the onward boarding, and those agents are probably more likely to waive any checked-bag fees.

As for security, if the first leg BP doesn't have Elite Access, have them try to get in flashing the 2nd BP.