Hi Seramera,
Congrats on doing all that already. That's really neat.
Many script variables are indeed used by the back engine. The scenario counter (General_ScenarioCounter) is used indeed a lot (for city destroyed and whether Iifa roots expand to post-Terra spots on the World Map, but also whether Garnet has long or short hair and surely I'm missing some). The friendly flags (FriendlyMonster_Progress and the first bit of Ragtime_QuizzSuccess) disable the possibility to encounter those friendly monsters. The pepper spot flags (Chocobo_ParadiseFound and Chocobo_MognetFound) change the appearance of the entrance on the world map etc...
The "General" variables are usually the ones used by the engine. It sometimes happens that the engine fetch local or global variables for "hotfixes", especially on the Steam version of the game. At the end of the day, that's very rare though so you'll most likely never get to one of these instances.
Here's an example of such hotfix that can be found in the engine's source code: it increases the score of the Blank sword fight minigame by checking that the field map is 64 (A. Castle/Public Seats), that the running script is a function of the object 4 (Code4_Init or Code4_Loop) and even the exact binary position of the code executed (after the normal score is computed but before the "SetTextVariable" line). So you can see in that example that hotfixes are very specific: you'll almost surely won't have issues because of them. Also, these hotfixes aside, script variables (local or global) are never used by the engine so you can't mess with it by using "VAR_GlobBool_1" especially if it weren't used in the field's script already.
I don't have a complete list of these hotfixes or how the engine uses general-type variables for purposes like the ones you spotted.
Unfortunatly, these uses are spread in the code and hard to interpret.
I don't understand your 3rd question. Ice Cavern's Entrance and Daguerro's field scripts should be editable like any other. I'll check if there is a problem with these but there shouldn't.
I am currently working on an update of the tool that will fix the issues with the field 70: Opening for FMV (among other things).
I don't know of a better way to check if the player character is in the region. I think that your solution is actually the best suited and fits with the spirit of programming tricks they usually used.
(By the way, Global-type variables can be used up to index 79. If you use "VAR_GlobUInt8_80", it will get out of the array range and probably at least throw an exception on Steam, effectively at least terminating the script function, or have an unexpected behaviour on the PSX version. I'm not sure if that limit is documented correctly in the tool.)
