Some (current) thoughts on this from an outsider:
First off, I'm pretty sure we should talk about individual Office365 Apps being MSIX or not, versus all of Office365 being MSIX. Each of the components under the Ofice365 brand have independent development teams within Microsoft, with their own set of requirements and priorities. Just think back to how the "ribbon" got added to office apps one at a time last decade.
There are, as of today, no Office 365 Apps that are released in MSIX form. Teams has been released as MSIX, but that's not part of Office 365 and was relatively new code. Microsoft has often said things along the lines of 'we realize how important it is for Microsoft to release Office 365 as MSIX', and 'The Office 365 teams are working hard on this', and 'we have nothing to say about when a release of Office 365 in MSIX will happen at this time'.
These statements are old. Surely there are issues with the teams getting this done. On a grand scale, existing first and third -party plugins would have to be redeveloped for a component to go to MSIX. Even the mechanism of attaching the plugins, which are currently in-process dlls, needs to be overhauled. For security reasons alone, these should be integrated as separate processes in the future to harden the office platform.
But whether the dev teams within the Office 365 org have the appropriate level of executive pressure to get something done in this space immediately is an open question, given the lack of externally visible progress.
Specifically, to answer the Pollewops question, a modification package for plugins would be the most appropriate method to package up a new style plugin, but only if it is a dll loaded into the Office 365 component process directly. The Shared Package Container (SPC) might be needed instead if exe plugins are the future. SPC is only available on Windows 11, so time would be needed to make that feasible anyway.