Mods aren't a headache for ED, they are a potential headache for users. As they are not official ED or third-party projects people use them at their own risk. So if an update breaks a mod, oh well that's none of EDs concern it is up to the mod community to fix them. If you had actually paid attention to the ED forum BTW you will see there is a modding section
https://forum.dcs.world/forum/69-dcs-modding/
Why not make the launcher with a built-in option to start other programs?