Are theses done in industry (French CIFRE) a disadvantage in academia?
From personal experience, and from an academic perspective, CIFRE theses are a mixed bag. In some cases the company is essentially not involved at all in the thesis (e.g., they have no clue how to get involved, and are just doing it for tax optimization purposes, to keep a link with the university/school, or even out of courtesy to them or in exchange for other favors) and then the CIFRE thesis is basically funding for a normal PhD thesis with a company involved on paper (and then you'd better have good supervision on the academic side, like for a normal thesis). In other cases, the company sees the CIFRE mechanism as a way to get access to cheap qualified labor, and overload the student with work which is not always in their best interest (e.g., not publishable), at the expense of their doctoral work.

The expectations around the mechanism are also very different from student to student. Sometimes the student really wants to work at a company, and just wants a PhD to improve their career prospects. Sometimes the student really wants to do academic research, and this is mostly a way to secure funding (which might even be proposed by the academic advisor in they are collaborating already with the company). Sometimes there's real scientific value in a mixed project involving both academia and a company: that's the ideal case, but pretty rare. Sometimes the student is someone from industry which is already used to a high (aka, non-academic) salary and a corresponding cost of living, and the CIFRE mechanism is one way for them to do a PhD without giving up on their current salary. And of course sometimes the reason is that the student is not ready to choose between an academic or industrial career and wants to do something "in the middle" to keep as many options open as possible.

I don't know so much about this mechanism but from what I've heard, I would recommend:


Discussing with the academic advisor and company advisor to clarify expectations: are they thinking that they would work together with you, or that you would spend your time between them, which kind of ratio, does the company have precise tasks for you that would be useful to them, which role would they take, etc.?
Being wary about PhD topics that crucially require input from the company (e.g., if your PhD is about analyzing company data, but the company isn't really committed to working with you on this, you could be stuck)
Probably making sure that you like what the company is doing and would like working with them, even for non-research stuff; or at least clarifying that you won't have to spend too much time on this if you don't want to.
Choosing your academic advisor and topic carefully, unless you really plan to do most of your work at the company and don't intend to continue in academia afterwards.


Good luck!