Cotton Original on PS1 is based on the arcade, but yeah it has weirdo remixed music. It's also missing the 2nd loop, and the first loop is considerably easier on defaults.
It also has some weirdo PS1 particle effects for the attack spells added to it. And an extra difficulty option that adds suicide bullets.
The PCE version is quite a bit easier then the arcade due to some exploits (PCE Dragon Boss has a safe spot where you can't get hit).
The X68000 version is a total remix with totally exclusive boss fights, lots of add parallax, tons of extra animation and the levels have been changed quite a bit. Overall I'd say it's an absolute must play for anyone that's mastered the arcade/pce versions. (Personally I really don't like the PS1's weirdo remixed music).