All destructive rendering of audio edits will create a new clip; there's no way around that unless you want to give up the ability undo destructive edits or close a project without saving and expect it not to be altered.
I know how much you hate workarounds, but maybe this would be more palatable:
- Mute the part of the MIDI clip where you want to have silence.
- Bounce with the time range extended as before.
- Unmute the MIDI as necessary.
But I'm a little curious about the meaning of "I want to modify that audio 'clip' by inserting a few seconds of silence at the end of it, so that I can use the underlying audio file and not have an abrupt ending."
How does adding silence prevent having an abrupt ending?