The sacred battle screen... or "why is it sacred"?
Because it been around for a hell of a long time.
In all seriousness, you're likely to have a load wait even if the battle system is on-map, unless it's an action RPG or whatever FFXII did. And the shatter effect replaces a load bar.
Programmers would save themselves hours of time
That battle screen is just an interface. Interfaces do not take that long to program. They take forever to design, but you're still going to have a battle interface even if it's not a seperate battle screen.
Also, your average 16-bit RPG didn't have any longer for a battle load-in or load-out than CT did. Yes, you switched screens in FFIV. And in CT you had a few seconds where everyone drew there weapons.
You could also get the same effect as CT by taking a temporary screencap, minus character and enemy sprites, of the current dungeon/town/wherever, load up a seperate battle screen, and then use that screencap as the background. Actually, I think that's how you emulate it in RPGMaker. Of course, if it's a DS or SNES game, you'd also want gratuitous mode 7 effects.
cause it's da seventh goddamn mode and u know dat turns u on
Unless it's like Tales of the Abyss where battles take forever to load it's kind of not an issue, at least from the reasons you're describing it.
Programmers would save themselves hours of time, and fans would have less to complain about if they just did away with the whole battle screen all together. To date, only ONE turn-based RPG has ventured to do this, over a decade ago, and it's been praised ever since: Chrono Trigger.
Septerra Core, Ultima 6, Fallout, Fallout 2, Arcanum, might and magic 3-5, might and magic 6-8 if you count their optional turn-based thing, Wizardry 8, arguably Phantasy Star 1 while you're in the dungeons, since it just overlays the enemies on top of the current view, Arc the Lad 2, probably the other arc the lads (and not the first one since there aren't areas you can walk around in), The Spirit Engine, the Avernum series (seperate battle maps if you're on the overworld, mind, for obvious reason), every roguelike ever (Except that crappy one that starts with an E or an L or something, and it's very yellow looking), arguably any first person RPG that behaves like PS1, actually...
* loads up RPGFan review pages *
Shadowrun on the SNES, Drakken, probably more that I don't feel like looking for right now...
Although the list is shorter if you remove games that let you move around in battle, and if that's the case, I'm going to say that having a seperate screen is probably the most appropriate design if your battle system just consists of picking menus from an option. And really, the fact that battles took place on the map in CT, instead of in a seperate screen, was more of a purely aesthetic thing with a very minimal affect on the gameplay.
In general the main reason for having a seperate screen is that, if your battle system uses a drastically different interface from the rest of your game, like most of the games using a seperate screen do, then you really don't want to overload your initial context. and in most JRPGs, that battle system and the rest of the game are kept pretty seperate.