Common sense would dictate that a field with a large difference in threshold elevations would lead one to set that in preference to field elevation, but. . . some companies discourage the use of common sense.
Can't help thinking that when Boeing wrote the manuals all those years ago, they reckoned that approximation was OK, if they ever gave it another thought, they probably came to the conclusion that the system wasn't so precise anyhow & left it at that ,as it had never caused any problems.
As the 2nd Q asked "preference" rather than procedure, well, easy one . . 40 every day.
Why ? aircraft is more speed-stable/less pitch sensitive on approach, if heavy, speeds are more reasonable, much easier to put the aircraft exactly where you want it on landing as the flare does not demand the level of absolute precision demanded by a Flap 30 arrival, so, less chance to either underdo it (crunch ! ) or overdo it (floating along) than F30.
As to crosswinds, well I have done enough x-wind landings on RW's short enough to encourage F40 (even if F30 was theoretically possible) to say, I never found the handling wanting with F40, & if gusty, much prefered the ability to put the damn thing on the ground,exactly where I wanted, rather than flare /float/drift/Ooops which I have seen a few times on 738 in gusty conditions, by my own hand & particularly by inexperienced new FO's.
Only 5000hr on 800, maybe I haven't hacked it yet