I've just built (using ./configure; make) 3.1a on FreeBSD 6.4 amd64.
libpthread is used by the resulting binary, not libc_r, according to ldd.

I would expect then that explicit action is required to use libc_r, and
given that FreeBSD people have indicated that it is deprecated and no
fixes are likely to be made, I would suggest documenting this as a
"don't do that" (ie use -lc_r) and close this as "won't fix".

The README file in the root of the source tree would seem an appropriate
place for such documentation, though I note that there appears to be a
lot of out of date information in there already...