Zachski: Huh, actually, that's pretty interesting. And if I had to guess, it only applies to the Paladin.
Here's why - in QFG3 and QFG4, a necessary workaround involved giving the Paladin 5 points in Magic in order to allow them to use their healing powers. This also forced them to learn the Aura spell in QFG4.
Since QFG5 uses a different engine entirely, it doesn't need to use this workaround. So in addition to expanding the repertoire of powers that paladins have, they also made the game check - if your magic was above a certain level (and I'm guessing the threshold is 100, thanks to your input) then it would allow you to keep your magic because you're obviously and intentionally a hybrid. However, if it''s clear you didn't use much in the way of magic at all, then it'll remove the skill and the spells so your character can remain pure.
To summarize, they did this to fix a previous workaround they had to use, while making a simple check to make sure they weren't stripping magic away from a hybrid character. You managed to straddle that line due to having some spells above the threshold and others below the threshold. I'm also guessing that it would automatically boost any spells that, say, a paladin with magic *added* at the import character menu would have.
The threshold is 50, actually. When working on what was happening in losing spells from QFG4 to QFG5 in speedrunning context, any spell with skill less than 50 was dropped from the list when heading into QFG5. Magic, because it isn't necessary, is actually the one core skill that doesn't get bumped up to a minimum level when importing in QFG4. The same goes for the individual spell skills. Any new spells you learn in QFG4 are at a minimum level of 100, but it won't bump up old skills. Some are very easy and fast to build up, like Open (just select the spell and click any random object; it'll continue to grind above 100 in a matter of seconds). Others, like Trigger (if learned in QFG1) start too low.
QFG2VGA fixes a bit of this because it brings in some spells automatically at 50 if you have magic but didn't get spells. Flame Dart, Fetch, Open, Calm and Zap (I think Zap, might be Detect Magic) are given at 50 even if you didn't buy them in QFG1, but if you did buy them and didn't level them, you don't get any skill bump. In QFG2EGA, you live with your decisions from the first game and do not get missed spells or a bump or boost of any kind.