I'm not 100% sure, but this occur because Dolphin doesn't emulate disc access delay (it'll just load the game data as fast as your computer can). In Metroid games, the data from the next scene/room is loaded in background, but in the real hardware, there's the disc access delay, so it takes some time until it's loaded. In Dolphin, there's no delay, so, the next door/room will be entirely loaded almost instantly and that's what causes the micro stuttering you're experiencing...
Avell A70 MOB: Core i7-11800H, GeForce RTX 3060, 32 GB DDR4-3200, Windows 11 (Insider Preview)
ASRock Z97M OC Formula: Pentium G3258, GeForce GT 440, 16 GB DDR3-1600, Windows 10 (22H2)
ASRock Z97M OC Formula: Pentium G3258, GeForce GT 440, 16 GB DDR3-1600, Windows 10 (22H2)