Recently I did an All Bosses Classic run for FDS Metroid in which I got 29:28.934, which is a bit faster than the cyberpod3's run of 29:29. But I observed that in cyberpod's run, it's running the Nintendo GameCube Japanese port of the game, where the loading times are much more shorter.

I did comparisons between it and the NESTopia UE 1.51 emulation where I run the game with, and discovered that in each of the seven areas where there's loading times (Entering Norfair, Entering Ridley's Area, Exiting Ridley's Area, Exiting Norfair, Entering Kraid, Exiting Kraid and Entering Tourian), from the first frame Samus disappears on the elevator to the first frame the next area is drawn, The NGC Japanese version takes between 2.817 and 3.000 seconds (with most areas clocking at 2.817 seconds), while on the emulator it takes between a whopping 23.941-24.191 seconds (with 24.066 being the most consistent clocking between areas).

By the end of the game, going with the most common clocking, the total time of loading adds up to around 19.719 seconds for NGC and 168.462 seconds for NESTopia (2 minutes 48.162 seconds).

Because of the big discrepancy of loading times between versions, I would suggest for future runs to maybe utilize the time NGC takes to load between areas, so that the timer between the different versions is as small as possible.