The gerund often means "the action of" and won't always mean the same as the noun. They can mean the same thing, but not always so.
In your case:
the code's implementation
The one doing the action "implement" isn't a person. Rather, "implementation of the code in the system" just means something like "the fact that the code is implemented" or the product of the implementation, which is the system or a part of it.
implementing the code
The subject doing the action "implement" here would mean a programmer or a team of programmers. It's pointing to the person doing it.
Another example where
Growing flowers is fun.
The flower's growth is slow.
Additionally, words don't always have both a noun and a verb. Sometimes, you don't have a noun, so you need to use the gerund, and vice versa.