Unfortunately MSIX doesn’t support ability to uninstall previous MSI package. So the transition is quite a challenge. What I did is that it’s only when the program launches, it will look for MSI packages and uninstall them. The installation itself won’t remove previously installed MSI (it will remove previously installed MSIX though)
So yeah, there is a logic within Manager to handle this. This is how Microsoft recommends it to be done.
MSI is really old format that was originally created (if I’m not mistaken) to install MS Office back in 90s. MSIX is modern approach.