People who become naturalized have to go through a specific process at some point. When did Cruz do this?
Congressional grants of citizenship are naturalization. The grant may or may not require condition precedent or condition subsequent, may or may not require an oath, may or may not require a process, may or may not require registering an intent to naturalize, and so forth. Congress may specify whatever requirements they want.
In order to have US citizenship recognized by the US government, he (or his mother) had to submit to adjudication before a qualified agent of the US government. This agent could be either the state Department, or Immigration and Naturalization (USCIS now).
If he doesn't submit to adjudication, his birth certificate proves he was born an alien of the US, and that is what he remains until proved otherwise. When proved otherwise, he will be naturalized, changed from an alien into a citizen.