One thing I've not understood about flatpak (or their competition for that matter) is why don't these permissions get prompted when they're used? Similar to iOS and Android, ping the user and confirm whether or not they want to give the application this permission. Perhaps even allow for customising the permissions (e.g. when it asks for permission to the homedir, you can override what the homedir would be when promp…
(Majority of) People barely understand the (privacy/security) impact of giving access to Location, Contacts, Calendar, Phone, SMS. Now think of the more obscure (?) layers of the following pyramid: Hardware, Middleware/Drivers, OS, Applications. (Majority of) People hardly understand Applications. You want to ask them if they can write on X folder? On the OS? Good luck!
Although both A&G can review your code and flag these upfront with some auto-policy-check, I feel that it would send many app creators reeling & pain. Pain for app creators = smaller revenue to A&G.
I assume it's the typical cat & mouse game. A&G may try to reduce/prevent access here but their SDKs will create a new oppotrunity/workaround to get access there. The new "there" access will be abused and someone will find away to do what they were doing in the previous setup. And thus we restart the chase.
It's in the way that people code. Naughty and/or lazy coders will go for the keys to the kingdom, ignoring the security. To avoid misunderstanding the word 'lazy' doesn't mean 'lazy people', but 'lazy/inapprpriate/corner-cutting practices'.