I believe for many companies, developers work on giant codebases with many hundred thousands or even millions of lines of code.
With such large codebase you have no control over any system. Because control is split between groups of devs.
If you want to refactor a single subsystem it would take coordination of all groups working on that part and will halt development, probably for months. But first you have to convince all the management people, that refactor is needed, that on itself could take eternity.
So instead you patch it on your end and call it a day.
Oh, and GBA rom is included with game files.