I've spent the last week learning the route for Normal Mode and I've come to realize that what looked totally random is usually scripted to some degree. I've got no lore names for these characters so I'm just using the stupid names I've heard for them in other playthroughs.

The Mole boss's bombs are random but somewhat determined by your position for every bomb beyond the first volley. His pattern for jumping out of the mole holes is always the same every single time.

Storm Eagle's Dad (TM) has a first phase where he dives at you in patterns that look like he's homing in on you but actually he always hits the same 3 areas. Same for the second phase when he goes offscreen and dives repeatedly.

Bubsy (boss of frozen palace) always does the same thing every single time so that fight is actually easy except that he's speedy and his hitbox doesn't include part of his head (you can more or less just do the TAS strats).

Dog Wizard has the falling spikes from the ceiling which are like semi-random. I don't understand how these are seeded because they're slightly different sometimes and they're slightly different in every video I watch but every I attempt to fight him they always drop in more or less the same pattern. Every other attack of his is scripted and even when he teleports and makes clones the real one is always the same.

Minor edit: I'm not sure but I think whatever the ceiling spikes use is seeded by time from power on to game start. Getting to Dog Wizard with a new game from power on, the patterns he uses will be different every power on, but then regardless of deaths or clock time or stepcount or even full-on game overs the falling rock pattern will always be the same. I haven't done any RAM analysis or anything so I can't verify any of this empirically but this is my observation from a couple hours of attempts.

Bernardo the Blackhearted (actual lore name what what) has what looks like the most random attack of all with the fireballs that cover the screen but having played the fight a dozen times now and having compared to 5 other videos the fireballs always hit the same screen areas. I still haven't learned this fight proper because it's basically a bullet hell but holy crap it is so comforting to know that I can actually learn where safe zones are in this fight.

Also, the stupid crates in The Final level always spawn in the same places but their spawn is dependent on your screen positioning which makes it very possible to manipulate them to maneuver through the level.

In general it seems like everything in the game is on local cycles except for the melting and refreezing ice in frozen palace which is definitely on a global cycle of freezing every 5 seconds and unfreezing 5 seconds after. I think the wires are on a global cycle too but I haven't nailed that one down.

As an update, I've found that the Mole Boss's bouncy ball's path seems mostly based on how much damage it's taken. At some point I'll make video of the patterns I've been able to find.