Is it possible to join academia with a structured PhD?
In practice the distinction is gradual. Some structured programs don't function as well as advertised, meaning that the PhD students are pretty much left on their own, while some advisors of individual PhD project are very structured. Sometimes individual PhD students can participate in (parts of) a structured program, etc. etc.

In the end if you get a PhD, then you got a PhD regardless of the type of program. No one will know, and no one will care one way or another. In practice a well functioning structured program is beneficial as the students tend to learn more and the network of a given cohort in such a program tends to help as well.