But given it comes with an .msi installer, I'm going to have to install Wine anyway before it will install. I believe.
I've paid for this Linux version, and support for it through these forums, not for support for a native Linux version of UAE, so I can't really expect help from this community or this author with that.
It may be helpful to look at this process in two stages:
1. The installation and initial configuration of AmiKit XE
2. Running AmiKit XE
Those two things do not have to happen on the same computer, because the outcome of Step 1 is basically an .HDF hardfile that you can move where needed so that you can get to Step 2 and run it with whatever will work.
I suggest that you take the MSI, and run it wherever you'll have the best chance of success of producing that HDF hardfile; then follow the steps in the link I posted, or the steps listed here: https://espenskogblog.wordpress.com/2019/05/13/amikit-xe-on-fs-uae/
If I were in your situation, rather than try and set everything up in a debugging-compromised environment, I would:
A. build AmiKit XE on a Window VM, then
B. create an Ubuntu VM, copy the HDF files over there and get it running under FS-UAE, and once I had the configuration settings correct,
C. take the HDF produced by A., and the conf files produced by B., copy them to a thumb drive, and then boot into Ubuntu on the VCS, install FS-UAE, and then try and run it.
Doing everything on the VCS seems like a drag