For levels where the timer counts down to 0, this causes the leaderboards to be in the wrong order, as 1st place has the least amount of time left, as opposed to taking the least amount of time. Is there any way of fixing this, such as subtracting the final time from the time given at the start to get the time taken, then ranking the leaderboards on that?

Developers of speedrun.com are working on that, and it will be included for In-Game Time levels when it is implemented. :)