Unfortunately, WiX is still a pain in the ass to use and there's a lot of simple tooling that makes NSIS/InnoSetup/etc shockingly easy to use while the same MSI experience is garbage.
Didn't they discontinue those around VS 2015 or so? Its been a while since I tried. Iirc that's what got replaced with WiX and ClickOnce, both of which are 100X more complicated to use.
Nope, it is the other way around, MSI became the official replacement for exe installers, and MSIX is the evolution of APPX from UWP/Windows Store and the "best practices" format going forward.
By VS packaging tools I mean tbe application project type that generates a MSIX as build outcome.
msix is just a different beast entirely too.