One of the two is part of a standard package that all Linux systems, and many non-Linux systems, have installed. The other is a special-purpose tool.
Your bet is irrelevant in the face of widely implemented standards. POSIX will outlive GNU coreutils. I'd bet your system also probably has a package manager that makes it easy to mark parallel as a dependency of your software.
>many non-Linux systems
Linux is pretty much the only system that typically ships GNU coreutils. The only one that comes to mind is Hurd.
For exactly this reason, GNU Parallel has the option --minversion.
So in your script you put:
parallel --minversion 20140722 || exit
if the rest of your script depends on functionality only present from version 20140722.
If the parallel in the $PATH is not GNU Parallel it will fail (and thus exit). If it _is_ GNU Parallel it will fail if the version is < 20140722 and succeed otherwise.