I want to create a silent installer without message boxes. Inno Setup gives you the opportunity to suppress these. Sadly there are default values and I don't know how to override them.
Here is the documentation from Inno Setup:
https://jrsoftware.org/ishelp/index.php?topic=setupcmdline
Example: I want to set "yes" if messagebox contains 'File exists, confirm overwrite.' situation. Default value would be "no".
Your question is imo moot.
By default, Inno Setup does not ask for overwrite confirmation. It asks only if you explicitly tell it so using
confirmoverwriteflag. If you do not want the confirmation, do not use the flag.