I can only speak for Flatpak, but I found its packaging workflow and restricted runtime terrible to work with. Lots of undocumented/hard to find behaviour and very painful to integrate with existing package managers (e.g. vcpkg).
The flatpak ecosystem is problematic in that most packages are granted too much rights by default.
I wasn't directly involved, but the company I worked for has created its own set of runtimes too and I haven't heard any excessive complaints on internal chats, so I don't think it's as arcane as you make it sound either.