In Matrix a direct chat is a group chat with two people.
You’re right, I forgot how Matrix handled messages and the current state is that there’s are at least 6 other clients that support E2EE - this is awesome.
That said, as soon as you look for a stable client that supports other features like Native 1:1 calls and Threads the only client listed is Element, check here: matrix.org/ecosystem/clients/
Side note: Looks like ~3 years ago a Fluffychat dev stated they would not implement E2EE in the app [0], this must have been around the time I was looking at other clients because I recall this one “looking” the best and might be viable for non-techy people to use/recommend. I’m glad they changed their mind and implemented E2EE. Time to take a look at it again.