If you go to the flight menu by hitting escape, the game pauses as expected, but from there you can use the time warp "," and "." (or "<" and ">") keys to make the game keep playing, and you can even fully control the craft; meanwhile there's just a menu overlay on the screen.
Also sidenote: apparently the bug report box is a bit buggy; if you copy-paste something into this box, and try to press backspace from the end of the text it's strage, there's some phantom spacing (it should be easy to reproduce).