I agree with the general principle here that sysctl changes should be in the place one expects.
I'll play a small Devil's Advocate here though: one thing I often do is use Puppet to "purge" directories of unmanaged files. For example, I purge the /etc/condor/config.d directory to ensure that old configuration files go away and nothing sneaks past me.
The sysctl.d directory is high on the list for purging files I don't know about. So, if the PID limit were really integral to how HTCondor works, I'd want it, and any changes, documented with flashing lights in all release notes.