That's the main reason we are using present tense in commit messages, not past tense. It's the commit that is applying the changes at that moment.
As a linguistic note, commit messages (at least, English commit messages) almost always use an infinitive verb and therefore may be considered to have no tense at all, though to argue that infinitives have no tense you do need to draw a distinction between tense and aspect.
You're confusing a bare infinitive with an imperative. Infinitives are often, but not always, marked with to. Commit messages are not commands and are not capable of licensing imperative forms.
Here are some examples of bare infinitives in English, with the infinitive form italicized:
1. This organization will help you apply for a loan.
2a. Q: What does he do?
2b. A: Check over the paperwork to be sure everything's right.
A commit message is doing exactly the same thing as occurs in example 2b.