Please correct me if I'm misunderstanding, as I'm not familiar with the system.
GPLv3[0] introduced protections again Tivoization:
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"“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM)."
You can install your own version of Git, yes. But Apple, as a distributor, cannot prevent you from installing a replacement for the software that it distributes. If, wherever they provide the source code to Git, they do provide a method to replace the currently install software, then that wouldn't be a problem.
