Not sure if the Meson is already ready to be used for CI. Ideally, the CI builds generate full installers in release quality.

I would say this is an argument against dropping autotools from CI. Either way, you want to test meson in CI because you do not want meson's support to regress, surely?

is it possible to build Geany-Plugins with Autotools against a Geany built with Meson?

I can't think of a reason why not. Surely, if both build systems install the same files -- which they do on Linux at least, right?

the Meson build installs the docs into the root prefix instead of share/doc/geany

This is a deliberate inconsistency, for whatever reason:

https://github.com/geany/geany/blob/7af6eafc0525bfafc8bdb2fbd29452b5f5409f56/meson.build#L137-L143

Maybe inadvisable, maybe it should be changed, but the current state of affairs is that meson has been instructed to do different things on mingw, so it does. This can be easily changed if desired. Perhaps it was unclear in the initial port what the optimal approach was.

the Meson build does not install libexec/geany/geany-run-helper.bat (for full details find the lift of installed files by Autotools and Meson attached)

This is pretty easy to do now that the concern has been raised.

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