My guess is, that this depends on the script itself.
If the script is written so that a timeout is critical you will have to change the script.
Some have a switch to change the behavior.
My 2nd guess: It is hardcoded
Couldn’t find anything in the docs.
If no one of the dev team reveals a way to change it, you will have to change every check command timeout by hand.
No, the point is that a script is not returning a result at all, and after 60
seconds Icinga itself is declaring a timeout, and saying this is Critical.
So, it must be something in Icinga itself rather than any specific script.