Thank you for contacting us for help, we apologize for the delay in response. Generally, if you would like to use an app that requires Passenger, I would only recommend you set it up on a new/empty website directory to get started.
WordPress is in fact a bit sensitive when it comes to sharing a directory with any other apps, and passenger would change their directory path as well (to /public). So it’s best to leave WordPress where it is, and perhaps create a sub-domain with its own directory (application.domain.com for example) to set up your Flask (or rails, or whatever else needs Passenger) app on.
Passenger should only be enabled if you intend to run a Ruby on Rails (RoR) or other Ruby/Python-based program as the sole application for the entire domain or subdomain. Passenger directs all requests for the designated domain/subdomain to the associated Rack-compliant application. So it's best to leave Passenger disabled if you do not actually need it.