If you're using the autosplitter it should also automatically pause the timer when the game crashes since you're no longer in a level, so the only time lost will be due to progress rolling back to most recent save.
Console commands are not allowed during the run (i.e. you can't tweak settings mid-run), aside from where explicitly noted in the rules. Some console commands are necessary before the run to set up the appropriate requirements (showing timer, limiting fps, etc).
Ornion is correct re: the reason for 125 max fps. It levels the playing field across most hardware. (Similarly, that's why we measure run times with loading time removed.)
Spin glitch takes one movement tech (elevation boosting) and changes it into a different movement tech (spin glitching) and the former is probably more fun due to the planning involved - the latter is just repetitious mechanical execution.
That's why spin glitch got split out into a separate category in the first place.
Rules for each category are viewable by hitting the "View Rules" button on https://www.speedrun.com/jka/full_game (make sure you have the appropriate tab selected for the category).
Sound is not mandatory but certain settings must be enabled - see the View Rules window for details.