make server: fix config setup for pkg build

When the server installs packages from source, it needs configuration
entry that points documentation indirections to the right place.
A relevant "config.rktd" is written, but to the wrong place, so
that it wasn't being used.

Merge to v6.0 (pending review)
(cherry picked from commit 9de2aff3f3c0842a1eb14efa5d0a88dc161de0b7)