Out of the blue, when starting FSX, I get requested to confirm or not the following programs...
Couatl Scripting Engine/ SODE / Addon Manager/ SimObj Animation Module/ FSUIPC4.
This doesn't have anything to do with GSX or FSDT since, as you noted, it affects all 3rd party installed modules. What's likely happened, is that some other installer, or you, changed this settings in the DLL.XML file
<Launch.ManualLoad>False</Launch.ManualLoad>
The one in the first section, not inside the various <Launch.addon> sections. It defaults to False, you probably have it at True for some reason. This will make the sim ask confirmation for *all* modules at each start.