RAW: Ambiguous

The rules are not clear on what, exactly, constitutes an “arcane spellcasting class” or a “divine spellcasting class,” probably because initially it was obvious. By default, assassins, bards, sorcerers, and wizards were the arcane spellcasting classes, blackguards, clerics, druids, and paladins were the divine spellcasting classes. There was no ambiguity: the former are the classes that cast arcane spells, and the latter are the classes that cast divine spells. Easy.

Then they printed things like Alternate Source Spell, Rainbow Servant, Sha’ir, and Southern Magician, which introduced ambiguity that hadn’t existed before. In these cases, you have spell slots from one class being used for either arcane or divine spells.

Does this new feature suddenly make the class into an “arcane spellcasting class” or “divine spellcasting class” where it wasn’t before? There hadn’t ever been a strict definition before, and they didn’t print one at this point, either. Some of these effects seem to try to include wording that prevents this kind of thing, but much of those rules are also unclear. For instance, consider this from Southern Magician: “The actual source of the spell's power doesn't change,” which Customer Service interpreted as preventing entry to mystic theurge. But it doesn’t really say that, does it? It says something about power source, which is unclear.

Unfortunately, there’s no direct, rules-as-written, “as it says on page xyz of Complete Shenanigans” kind of answer to this question.

Recommendation: Never

RAW is ambiguous, but what’s going to work well in-game is not: never, under any circumstances, should one be allowed to advance wizard spellcasting faster than the wizard does. That should never, ever happen in any game, and if you’re going to allow it you might as well allow Pun-pun.

Allowing these sorts of tricks to qualify for mystic theurge, and other prestige classes and feats that require one type of spellcasting or the other, is pretty clearly legal, RAW, and also usually far less troublesome. The only exception I’d be likely to make is the dweormerkeeper from Complete Divine’s web enhancement, but then I’d probably just ban that class outright.

Even allowing a divine-only prestige class to progress wizard spellcasting is almost-always not a problem. It’s the double-progression that should never, ever happen.

Strongheart vest provides “Ability Damage Reduction”

The strongheart vest soulmeld from Magic of Incarnum reduces the ability damage you take by 1. Requires the Shape Soulmeld feat, which requires Con 13. Which anyone should have that isn’t undead.

Naberius, the Grinning Hound provides Fast Ability Healing

If you have a single level of the binder class, you can bind Naberius, the Grinning Hound to get the ability to heal ability damage at a rate of 1/round instead of 1/level.

Rod of bodily restoration is the most cost-effective item to heal ability damage

The rod of bodily restoration from Magic Item Compendium has 3 charges per day, can spend 1-3 charges to heal physical ability scores. Does not work for mental scores.

That said, metaphysical spellshaper is a ridiculously broken class

Metaphysical spellshaper is like an incantatrix on crack. Incantatrix, one of the highest-power prestige classes in the game. And you could have levels in both. I strongly recommend against playing this class. It is not well designed, and you will be vastly more powerful than almost anyone else could ever be.