The CS issue is only seen when you try to use an eboot.elf that is built from scratch.
The eboot.elf checked in works fine. The .text section is significantly smaller than the one built from scratch.

Added dependencies for eboot.ld and Makefile to Makefile.
Updated eboot.ld to not fill with zeros through the CS field
on its way to the CRC.
Added size test to elf2bin.py

Edited: clarification