science/rdkit: fix build on GCC architectures

This port needs new GCC to build.

It adds -mpopcnt to *FLAGS, which breaks build on non-x86. Since it optimizes for the host CPU, don't enable it.

Some libraries are not installed on big-endian systems.

PR: 239299
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20997