She’s tall but she’s way too narrow to actually fit the shoulders on the suit. It’s one of those weird game oversights, like how many game building interiors are too large for the exterior to contain.
I don't think it's an oversight as much as it is simply the design of the suit to have large pauldron-like shoulders that also make it look like mechanical joints. And I mean, the biggest "how does that work" thing for me has always been the morph ball. How does she not just liquify?
My absolute favorite thing about the morphball is that even in canon it's a total mindfuck that makes no sense. Very light lore spoilers for Metroid Prime 1:
spoiler
There's a couple of research scans that essentially describe Space Pirate reverse engineering of Samus' morphball tech that basically say "This morphball shit is a lost cause. All our test crew have ended up as extremely dead pretzels. We should just quit while we're behind on this one."
The morph ball is usually half the height of samus' full sprite, which would make it a whole meter in diameter (iirc super metroid is the only exception). Most people could fit in that comfortably.
Actual models vary pretty wildly by game (out of suit for Other M has her quite short compared to other people), but I believe the only official height and weight comes from the Super Metroid player's guide (and more vaguely in the Metroid 2 manual), which says she's 6'3" (190 cm) and weighs 198 pounds (90 kg) without the suit.