Yes! No warnings related to this are printed. There is only one that you can see below.

eps.c:879:29: warning: implicit conversion from 'double' to 'long' changes value from 0.1 to 0 [-Wliteral-conversion]
1 warning generated.

I just checked the './configure' step using Gnuastro 0.21.70-5005 on a macOS Monterey 12.3 (Apple M1 chip). Below are the lines containing the string 'pthread'. I think the problem has been fixed. Let me know if you need any further check.
 

checking for pthread.h... yes
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for pthread_barrier_wait in -lpthread... no
checking for pthread_sigmask... yes
checking for pthread.h... (cached) yes
checking for pthread_kill in -lpthread... yes
checking for pthread_t... yes
checking for pthread_spinlock_t... no
checking for pthread_rwlock_t... yes
checking whether pthread_rwlock_rdlock prefers a writer to a reader... yes
checking whether pthread_create exists as a global function... yes
checking whether pthread_sigmask is a macro... no
checking whether pthread_sigmask returns error numbers... yes
checking whether pthread_sigmask unblocks signals correctly... guessing yes
checking for pthread_atfork... yes

Is this just an issue on MacOS? Using the tools on Debian Bookworm (clang-14). I don't see two '-pthread' options. I do see something like '-pthread -lpthead' but this does not show any other warnings.

Also I don't see the ld warnings that a directory was not found.