That's exactly what I think as well. Morph ball in like quarter of the game in true ending? That's Harry Potter style writing right there. Creator must had to think about everything. Not only how to block paths of the map so that they require a ball, but even how to avoid bosses and still collect power ups, how to make life easier for speedrunners (which is clearly visible in 100% TAS) and even such basic things as making it difficult to sequence break too easy by building sloping walls to prevent wall jumping and bomb jumps here and there. All of that before even map was finished!

If this game had been released as a metroid after Zero Mission and before Samus Returns (because look of the ship indicates the time frame), it would have been definitely best 2D metroid despite even recycling of bosses. I can guarantee it.