I´ve been doing some research for a solution that would use beacons but there is one thing that i dont quite understand yet. I have made some test with Googles open source beacon app for deploying and registering beacons and that was no problem.
This solution that I´m researching for would use an app for deploying beacons and that also means that they would be owned by the namespace of that app. There will be another app that would be used by customers but this app was not the one that registered the beacons and uses another namespace, how can this app discover the beacons? The beacons will not public.
Am I thinking about this in the wrong way or is there a more of a correct way to do this?
Beacons broadcast their namespace + instance IDs for every device around them to see. So it’s hard to speak of “ownership” here—everyone can discover such beacons.
You haven’t said exactly which app from Google you’re talking about, I assume it’s this one:
This app registers beacons in Google’s “Proximity API.” I’m not 100% sure, but I think that only the person that registered the beacons in that API can then retrieve the data back, so here there truly is a notion of “ownership”—but it’s less “beacon ownership,” and more “Proximity API data” ownership. So for example, if you register your beacons in the Proximity API and add some attachments to them, I think only you will be able to retrieve them. (Again, I didn’t play with the Proximity API too much yet, so I’m not 100% sure here.) But because beacon still broadcast “in plain text,” other apps can still discover them, just not access the Proximity API data.
And just for the full picture, with most beacons from most vendors, there’s another concept of ownership: i.e., only the owner of the beacons can connect to them and re-configure them. At Estimote, we assign your beacons to your Estimote Account when you buy them, and you need to use your credentials to connect and change their configuration. But this type of ownership has naturally nothing to do with Eddystone specifically. 
Finally, with Estimote Beacons, there’s also a feature called “Secure UUID,” where the IDs broadcasted by beacons are encrypted, and the keys to decrypt them are stored in Estimote Cloud, only for the owner (as defined immediately above) to access and decrypt. You can also temporarily grant access to the beacons to a 3rd party app via a feature we call “Infrastructure Sharing.” More info here, if you’re interested:
https://community.estimote.com/hc/en-us/articles/204576027-What-is-Infrastructure-Sharing-How-to-share-beacons-