Address the warning regarding duplicate option 'GEOM_PART_GPT' when
configuring kernels for i386, amd64, and arm64.
The 'GEOM_PART_GPT' option was added to the DEFAULTS configuration
in r337967.

Approved by: re (kib@)
Reviewed by: ler@
Differential Revision: https://reviews.freebsd.org/D17458
Sponsored by: Netflix, Inc.