1. There is a chance that if it thinks you've been defeated, it will end the timer. However, if the cutscene happens anyway I'd say it's unlikely. This is definitely worth a test though.

2. There are also things to take into account like lag on loading times and general frame rate drops if you want to go without the in-game timer. Many of my old runs were done on an old, weak computer, so some do contain noticeable lag (take Allies Mission 9 for example). I reckon the in-game timer is the best option we have available as it removes any sense of ambiguity.

I did just do some testing on this; Poochies's run was about 2.6 seconds faster than GBHmichael's. I'm thinking the game measures in-game time by frame count, so a slower computer would have the in-game timer run slower. The site's milliseconds option is frustrating. It has to be enabled for the entire game which can look ugly, and in cases where a time is exactly x seconds, it doesn't display .000 on the time. It got to the point I had to forgo recording milliseconds on the site and just measure them on a local database I have.

[quote=GBHmichael]Many of my old runs were done on an old, weak computer, so some do contain noticeable lag (take Allies Mission 9 for example). I reckon the in-game timer is the best option we have available as it removes any sense of ambiguity.[/quote]That seems contradictory. A slower computer would have the benefit of letting a runner have more time to react to situations. That's part of the reason why I opted to use in-game RTA for the rest of the series, letting it account for things like pausing.

Mario Kart 64 is infamous for this because of the PAL version running slower yet still altering the times to compare to NTSC, despite how they're not comparable.

One thing that I have noticed is that if you load a game from a save state, the AI acts differently to if it was played in a single segment. Certain events won't get triggered (like a certain enemy army moving to a certain location) etc. I haven't looked too much into strategic uses for these, but it would be an argument in favour of having an outside timer.

A timer on any speedrun is greatly encouraged when possible, regardless of timing method. When a timer isn't visible, frame count is usually accurate enough but requires more work on moderators (and possibly manipulable).

For now just enter in in-game time, the rest will be sorted out soonish.

By the way, adding a timer ¤after¤ a run is rather pointless. It's having a timer during the run that's important. I suggest using LiveSplit for that.