You are right that it is a limitation of the engine, hence why I am counterbalancing it by save scumming. I supposed I could always save scum and keep the scroll for another level if I failed the roll the first time around to be a little more in the spirit of 2E RAW, though. As for it being a BG rule, I am fine with deviations from the original 2E rules so long as they in some way improve the game, and a lot of the deviations the IE makes are questionable at best. For instance, having the scroll go up in smoke like that only serves to make things needlessly punishing, especially for some of the rarer scrolls *cough*breach*cough*.
Then, on the other end of the spectrum, there's the mess they made of the resurrection system that, oddly enough, was detrimental in that it made things too easy; fun fact, under 2E RAW, a character's constitution has a lot to do with coming back from the dead. The original constitution number is the maximum number of times someone can come back, each time they do come back they lose a point permanently, and once it gets below a certain level, you have to roll d100 to see if the character survives the resurrection (which gets harder the lower your constitution gets). Naturally, all of that was contingent on finding a cleric who could cast the spell needed (which required thousands of gp worth of diamond dust), having enough money (that diamond dust doesn't grow on trees), and the cleric actually wanting to bring the character back (which, if you have a nasty reputation as a heartless asshole, won't always be the case).
IE games, on the other hand, made coming back guaranteed (which was a nice touch, admittedly) so long as you had an intact body and gave the paltry sum of a few hundred gold pieces to the local priest who could care less if he was bringing back Bhaal himself; it was so effective that it raises a plot hole by making the player ask why in the hells they didn't try to raise Gorion, or anyone else who died in that game. Whereas 2E made death actually have lasting consequences and plugged plot holes like that, BG makes it easy as a way of counterbalancing the questionable encounter design (seriously, who throws this much combat at a level 1 party without trying to get a quick TPK?) . Still, I have heard rumblings of a mod that addresses this to a degree, so I may need to look into it the next time I take it into my head to play BG2.