I am refusing to accept the idea that it is hardcoded with pixel perfect locations in the code

For example boss movement, then when the boss stage changes, some parts are animating, decoupling from main body, etc. that sort of stuff.
Also intro animations, animating all of those sprites, it looks like procedural, usually its only linear movement of planes.
Any clue would be appreciated.
PS: I am developing a retro shmup and I want to use the old workflows with some extra help from today's libs of course. I might end up just using json hot-loading for animations, and just modify numbers (keys) until the animation on screen looks right

Thanks