The Flatpak is official.

# apt apt install
E: Invalid operation apt

the hidden “trashbin”, .Trash-$(uid), invented by Ubuntu

This isn’t some “idiotic principle invented by Ubuntu”, it just follows the freedesktop.org Trash specification. For many users, it can be really beneficial, see also the spec’s introduction:

An ability to recover accidentally deleted files has become the de facto standard for today’s desktop user experience.

Users do not expect that anything they delete is permanently gone. Instead, they are used to a “Trash can” metaphor. A deleted document ends up in a “Trash can”, and stays there at least for some time — until the can is manually or automatically cleaned.

Whether an application like Prism Launcher should use the trash can or delete the files directly is an entirely different question.