Looking at Alexander, let's ask ourselves this: if more of the magic damage was shifted to be physical, would there be any easier of a time clearing these harder floors? The answer is no. While PLD would have the survivability they'd lack the damage. On the same note, while DRK would have the damage, they'd lack the survivability. In fact I think that we would see even fewer groups that have cleared A3s and I don't think A4S would have been cleared at all if that were the case. The reason is because the DPS checks are so obnoxious that even doing mechanics correctly is not enough to deserve a clear in the eyes of SE. While I think it's okay to have an enrage timer, I do not think it is okay to have them as tight as they are on EVERY SINGLE FLOOR. It would be fine if there was a tight check on one floor (kind of like Patchwerk from WoW's Naxx), just to make sure you can do it. In fact I thought that's what Faust was supposed to be. I don't think PLD is bad, I think SE made a poor design choice by making an entire raid that catered to the flawed kit of DRK which in turn created the illusion that PLD was somehow awful.
Ask yourselves this, if PLD did receive buffs but SE continued to make the rest of the floors like A3S and A4s would it change anything? Personally, I don't think so. What if they made it so that everything was mostly physical again and lowered the tight dps checks while placing more of an emphasis on mechanics? Then we'd have the same issue we do now, only the shoe would be on the other foot.