Why you are reporting this is as a problem ? The message is correct, and the problem was that *before* the installer failed to alert you about that, like it always did for FSX or P3D. We just fixed the installer bug that it didn't alert you of not updating with MSFS.
Fact you were able to do so (because the installer didn't check) didn't mean it was safe to do so, especially after having added seated passengers, which need to modify not only GSX own files in the Community folder, but also other airplanes too, it became even more important to verify you don't do the mistake of updating with the sim opened, because ever change of any file in the Community folder requires restarting the sim, and this is of course common knowledge.