With this behaviour I cannot run a script with different flags without having to modify it if it contains a shebang lines with flags.

You could also argue the other way round, i.e. it provides for consistency independently of how exactly the interpreter is being invoked — in particular as there are some operating system that don't handle shebangs (one rather commonly used one is among them...).

And some options might be an integral part of a script, or at least important to its proper functioning — like -n, -p, -l, -C (which didn't work on the shebang line until recently, btw), etc. — so I would rather want them to remain in effect when I call the script as perl myscript.pl .