Are there any other instances of battle scripts altering enemy stats during a battle …?
Many.. I'll post them later when I get the chance.
The best representation of it is the Octomammoth. For every 1/8 of its HP lost, its Agility changes (and slows the monster down as a result).
Barbariccia's original spin form (in the Tower of Zot) makes herself immune to
any magic, which would have made "the old man" useless anyways.
Having said that, Protes and Shell work perfectly fine, so you’d think this would too.
Dude, this is the same game that took until the Euro version to fix the Yang HP growth bug or the Poison resistance bug.
It probably matters little in the scheme of things, anyway, since Caggy has multi-Boast’d Thundara to deal with by this point. 
Believe it or not, Tellah's Thundaga is far stronger than Palom's maxed out Thundara. A maxed out Palom with Quake would do better.
Palom with Thundara:
(64 (base magic damage) * 2 (weakness multiplier) - 48 (magic defense)) * 25 (spell multiplier) = 2000 damage minimum
Tellah with Thundaga (using Change Rod and Wizard's Hat from Mysidia):
(256 (base magic damage) * 2 (weakness multiplier) - 48 (magic defense)) * 7 (spell multiplier) = 3248 damage minimum
Even if you use Tellah's default equipment (with no stat boosts), it is still better than Palom's best...
(256 (base magic damage) * 2 (weakness multiplier) - 48 (magic defense)) * 5 (spell multiplier) = 2320 damage minimum
Edit: It's not a battle engine bug, but apparently I forgot that the game uses tables for pretty much everything (attack, defense, magic defense, and agility) except monster Magic Power.