Haven't been on here in awhile but decided to drop in to offer my thoughts after I got an e-mail notification. I actually signed up for the November cohort, so I haven't started yet and can't help you out here.
From my research, I will say that I did read similar criticism of (I think it was) General Assembly's UX programs, and how it was easy to spot the capstone projects in a portfolio. I imagine most of these boot camps will have a similar problem, even though some of them allow you to choose from a selection of projects to work on.
I think you just have to decide what you are looking for and find the best value you can get. For me, I am looking for the best way to build UX knowledge and skills from basically nothing so for me, UX Academy's stated curriculum, pricing, and guarantees seemed to be the best fit. If you truly need one of a kind capstone projects, I think you might need to look into more traditional (and expensive!), in-person programs.
Best of luck!