If we are talking about the security of a messaging system, then the only thing that matters to compare, is the security of the messaging system, not any particular implimentation detail.
All messaging systems are "comparable". If one relies on a secure enclave and one does not, it's hardly any more different than if one is painted yellow and one is painted green.
Messaging apps on phones painted blue and with tyre inflators are exactly "comparable" to ones on phones painted yellow with secure enclaves.
