The significance of Congressional authority over citizenship granted at birth to those born abroad is, according to the Rogers v. Bellei SCOTUS decision, that such citizenship is not a constitutional right, can be denied or revoked, and can be subject to certain requirements.
The same does not apply to 14th Amendment citizens who are born in the United States. Such persons have a guaranteed constitutional right to their citizenship and no action by Congress (absent a Constitutional amendment) can deny such citizenship, revoke it without a citizen's consent, or attach requirements to retain such citizenship.
That is a significant legal difference between a natural-born citizen under the 14th and a statutory natural-born citizen (citizen at birth) under the INA, don't you think?
For the sake of argument, assume that a citizen at birth (under the INA) is POTUS and Congress then passes retroactive changes to the INA that make that person a naturalized citizen instead of a citizen at birth. A mere legislative change by Congress can make the POTUS suddenly ineligible to hold the office to which he was elected. (Admittedly far-fetched, but you get the point, right?)
Nonetheless, a statutory natural born citizen, when the question of presidential qualifications is addressed, can check the box "yes, I am a natural born citizen."
So, to the question of Cruz's eligibility, the answer is: He is eligible.
Some compare that to the case of Obama, and that's ok. The rap on Obama, though not proven, is that he was born outside the USA before his Mom had fulfilled the 5 years after age 14 residency requirement.
There is absolutely no way to prove that about Obama that I can see.
There have been no statutory natural-born citizens since the 1790 act, repealed 1795.