The safe mode is a mode where you can e.g. possible revert some settings, get the app running because possible caused mods are not looaded, etc. . Thus, these dialog seems fine and is a usually pattern to do it in such way.
If you allways get CTDs its better to find out “why” , I get usually zero of it. As example if you know that a mod cause it, how it sounds in your case, ask the developer of the mod about a fix.
If you don’t like the dialog itself, you can e.g. create a script which removes the file: running.lock. Without these file MSFS assume all was fine before.
Not exact same as what you request, but bit similar and some background infos, you can find as example within these wish:
( e.g for MS-Store and Steam is mentioned where these file is located , shortcut to steam )