Do we think that the Hundred/Heli Gunner battle should have had the Still More Fighting theme play?
I think the Cloud / Rufus fight might have lost something if it simply repeated the music from the Heli Gunner.
Also, the EXP AP and GIL for Hundred Gunner are not earned, I'm guessing this is because of the fact that the game uses "Next Arenas" for the battle? Or is it because the battle doesn't end upon killing that enemy, the same as other enemies that "transform"? In fact, thinking on it, what exactly is controlling the deactivation of Spoils earned by Enemies after a transformation? Why exactly is it that the Hell House (for example) does not give spoils for killing both versions?
There are quite a few questions here. It's been a long time since I looked into FF7's scripts (5+ years), so my memory is quite hazy, but I'll do my best to answer.
Hundred Gunner / Heli Gunner don't work the way Battle Arena does. The arena is implemented via field scripting: field code can start battles and pass a bit flag to enable various battle mechanics features, one of which is a continuous multi-formation battle with player prompts every victory ("Off course!"). By contrast the Gunners (and things like Hell House) are implemented via battle AI scripts which enable / disable units in the same formation and copy over a struct of associated data (so that the game can simulate continuity in terms of statuses, stats multipliers - etc)
I don't remember researching how exp is gathered at the end of a battle. I don't think the Exp screen is actually part of the menu modules, but I may be wrong. If it is not a menu then it will presumably be powered by BATTLE.X. Looking at Proud Clod, there seem to be some actor flags (e.g. 4022/4024) that typically get set when those 'transforming' enemies die - my guess is that the battle engine uses these to determine whether a unit should be included in the exp calculation. I'd suggest should sniff around Battle.x to see what functions get called at the end of a battle.
Curiously enough, you can actually alter exp / ap / gil rewards for an enemy with AI scripts directly, but I'm not sure if any enemies actually do so.