I can offer a little perspective on MSIX, having devoted months of my life to it in a past job.
MSIX is nearly unusable outside the Store. It will work in a tightly controlled environment, but when you try to deploy it to a wide variety of users you will run into 1) unhelpful errors that basically can't be diagnosed, 2) enterprise environments that cannot/will not allow MSIX installs. I get the impression that the MSIX team is uninterested in solving either of those issues.
It's not a coincidence that virtually no first-party teams use MSIX to install their product outside the Store. Office tried for a while and eventually gave up.
Despite all that, there are still a few people at MS who will tell you that MSIX is the future. I don't really understand it and I assume there's a weird political reason for this.