freebsd-update: Swap pkg(8) flags in check_pkgbase()

Unbootstrapped pkg will ignore -N if -r is specified first. Flip the
order.

Prior to commit 66c75fa63aff this worked by accident.

Approved by: re (cperciva)
PR: 290393
Reported by: olgeni
MFC after: 3 days
Fixes: 66c75fa63aff ("freebsd-update: Fix the pkgbase check")

(cherry picked from commit 645352316be6901077dc1a3ce26f41934136f412)
(cherry picked from commit addc0556ce547425f9810fe081b46e8472340333)