Set execution bit in AtomicFileCreate itself and not afterwards.

[DailyDreaming]

@adamnovak made a good point: What's the point of atomically creating it with the right contents if the metadata isn't also part of that atomic operation?

See: https://github.com/DataBiosphere/toil/pull/3437

┆Issue is synchronized with this Jira Story ┆friendlyId: TOIL-809