I don't love FIPS either, but cryptosystems don't work the same way as buildings and electrical codes. It's very easy to have "secure cryptosystem A" and "secure cryptosystem B", and then have massive security holes in "cryptosystem A + B". This happens all the time, and is one of the main reasons for the classic "don't roll your own crypto" admonition. The FIPS "whole system" mandate is meant to forestall this failure mode.