I downloaded and installed the latest ALTA app (iOS) last night (I think it is 1.5), and the GPS height assist is missing in mine when I connect to my ALTA 6, too. Maybe Freefly forces the feature to OFF just so that people don't make a mistake.
Thanks Steve, it's reassuring to know it's not just me & therefore something which will be fixed with a software update
The GPS Height Assist option has been removed from apps connecting to new firmware, it is being reevaluated/tested & may be reintroduced in a later update