Bloodstained is an incomplete game (Full Game Spoilers)

I wouldn't go as far as to say incomplete (90 hours in and still not bored) but I do agree that there are signs of cut content.

I agree about Focalor, it just lines up way too cleanly.

One-off mooks aren't all that uncommon in IGAvania's pretty sure OOE had enemies that were restricted to post-game areas and there is one that comes to mind that only shows up in one room (I forgot the name though).

I also think there was meant to be a third-endgame area between the den of behemoths and glacial tomb but not for the same reasons you suggest, sharp transitions are things IGA has done before. My current theory is that it was a gambling themed area where you would fight Valefar while the Den would have its own boss. This is supported by some early info that bloodstained was supposed to have gambling themes which don't exist in the final game outside of Valefar and a backer room (which doesn't count).

The race is fine imo. It very much feels like something they designed so it could be put just about anywhere. Although if you combine it with my theory about the third end area then chances are it would be there as a sort of analogue to real-life race betting.

I do agree that Secret Sorcery lab is something that was made after the train. Like they knew they wanted to do the train but didn't really think of what to do after it, maybe in the initial plan it was meant or it to take you to the Den of Behemoths or something.

I don't think they'll re-add the cut areas and if they do add no areas they way to get to them will be the same as the Gremory portal/8-bit nightmare rather than as a part of the castle. 

Ok I need to get this down, so my current theory on the initial order plan:
Everything up to Valac is the same as the original plan.
Instead of Valac giving silver bromide, the secret sorcery lab (or its replacement) would be to the right of the towers
Then everything is the same till Gebel except you get aqua jet from Focalor after draining the blood fountain.
Instead of slashing the moon you would instead take the train to the final section which would be a gambling area, Den of behemoths, and finally the glacial tomb (albeit expanded)

Unfortunately this cuts out the photo ID thing (which I like quite a bit) since I believe Dominque is meant to be gone after the Gebel fight (instead of dissapearing after the Alfred cutscene). It also means that OD would be completely missable.

EDIT 2: Just read the backer artbook and