Ok, I found another "solution" to the problem of executables listed in the exe.xml file not being executed when firing up MSFS, including Couatl, and it is definitively contra-intuitive: you need to modify your .exe properties as such as that it is NOT(!) started as administrator. The moment I removed the checkmark for Couatl64.exe, it fired up again with MSFS as it should.
So, for anybody still having troubles that Couatl is not automatically started with the sim, try once by disabling the "start as adminstrator" on your Couatl64.exe and see if this cures your issue as well.
BTW: this was posted on Reddit by someone, is not my personal find. But it works on my end as well...