Okay, I've gathered enough information now from the game's code and Lemmix's code to understand all the timer-related differences, and unfortunately it doesn't make my job very easy:
A) It turns out that right now, the entrances are being opened in Lemmix a frame earlier than in the actual game. However, Lemmix also cuts off a frame earlier than the actual game when you run out of time. So the total number of frames given, not using the pause trick, is the same, but nonetheless, this discrepency obviously affects what you see in the game timer (a solution that seems to just make it before going from 4:30 to 4:29 would, in the actual game, hit 4:29, because of how the entrances are being opened a frame too early in Lemmix).
B) There's a further twist though with the actual game. When the game decides it's "done", as a result of either no lemmings left, no time left, or the user pressing ESC to abort, it doesn't immediately declare "abort". Instead:
1) it sets a flag signaling that it's now in the "fade-out" phase
2) Then in the next iteration, it starts carrying out the fade-out
3) then it continues to do one frame of lemmings updating,
4) and then just before running the code for updating the game timer, it checks if you're in the fade-out phase. If you are, it skips over the updating of the game timer, and either jumps to the post-level screen if the fade-out finishes, or continues on for more iterations of lemmings-updating (ie. back to step #2) if the fade-out is still in progress.
Now, on the "PC-compatible" mode with the "fast" fade-out, the fade-out is done within a single iteration--nothing is being updated during the fade out. (In other words, the complete fade-out sequence happens entirely within step 2, putting the game loop on hold while it's going.) However, as detailed above, after the fade-out is being carried (ie. the screen is actually black), the remaining portions of the game loop will still update the lemming before going to the post-level screen, but the game timer is not updated. This means pressing ESC at the right time, you can preven the game timer from going down another game second even though it normally would've.
Of course, the real advantage comes with the "High Performance PC" mode with the "slow" fade-out. The slow fade-out is done over several frames (I haven't determined yet how many, but it could easily be another game second). In other words, in that mode, the step #2 above in each iteration just does a little more of the fade-out, and the whole fade-out sequence is spreaded over several iterations. During all these frames, as noted above, lemmings continue to be updated (and you can even assign skills), but the game timer is not updated. So instead of holding off the game clock by merely one frame, the ESC abort can actually hold off the game clock around 1 game second or so in the "high performance PC" mode.
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All of this means I've my work cut out for me in getting Lemmix to a state that supports all these "special effects" related to the game clock. Even if I ignore high-performance mode, the regular mode is still already off by one frame in terms of the game clock (w/o the pause glitch), and there's the matter of ESC "holding off" the game clock by one frame. Even if we ignore all these silly "game clock" shenanigans and just go purely with counting number of frames (kinda my preference now actually since it's frankly a more honest indication of time compare with the timer, given all these idiosyncracies), I would still have to at least provide a way to show the frame counter in-game. I also need to be careful that my changes don't invalidate existing replays--for example, merely making the entrances open one iteration later would cause existing replays to be all off by one frame, which could be disasterous. So I would also need to compensate by putting an adjustment factor between the iteration number stored in the replay, and the actual iteration counter value in Lemmix.
Frankly, at this point I'm far more likely to get the "easier" stuff out of the way first, like the one-frame reverse, proper fake object, entrance trapdoor inert trigger area support, and resetting level number to 1 on changing difficulty ranking.
