Using drupal is a lesson in understanding others. But designers are a different beast. They don't understand the challenges we face if we need to recreate exactly what they want. That's where the hook for altering a form comes into play. It's all code, but very structured.
There are a many issues that may arise when modifying a form from within a custom module, but with patience it can be done.
It's a challenge to say the least, but the builders of the system thought of 'fun' ways to control the chaos.
There are a lot of tricks for solving these issues. Depending on what your situation is, some may be better than others.
Not that I'm going to list them here, hopefully in another post.
Now, I just want to share a graphic...