hmolina wrote
The .mobileconfig profiles do not have cert/key/ca fields.
I don't understand what you mean when you say that the .mobileconfig files do not have these fields. In a .mobileconfig file, the certificates are embedded as payloads between <data> and </data> tags. Is that what you are doing? There is online documentation, e.g.
https://developer.apple.com/library/content/featuredarticles/iPhoneConfigurationProfileRef/Introduction/Introduction.html. Are you making the .mobileconfig files by hand, or are you using the Apple Configurator?