Armor through base stats is 44% higher on melee champions (~75 vs. 52), and 150% higher on ranged champions @18 (~75 vs. 30).
You're talking a whopping 3.25 MR bonus in a base 52 vs. a last-whisper penetrated 48.75 armor on a melee.
3.25
Magic damage also has an 18.75 advantage vs. armor in that case vs. a squishy.
Armor is also easier to itemize for, what with having two 100 armor options and a solid 70, where MR is only available at most in 60 on 1 item and 55 on most solid MR items. Barring a Howling Abyss exclusive MR item at any rate.
With magic damage of any kind you're pretty much always going to have a free Last Whisper bonus.
The reason to avoid itemizing magic damage on a physical champion is never, and has never been, a lack of magic penetration.
Magic damage is essentially physical damage with free armor penetration.
The reason to avoid itemizing magic damage is because it almost never scales with critical strikes, attack speed, life steal, AD, armor pen, or apply on-hit effects.
It's a matter of
2 x 2 x 2 x 2 = 16
vs.
2 x 2 x 2 + 2 = 10.
Compared to something like GA though, it's more a matter of
2 x 2 x 2 x 2 +** 0** =16
vs.
2 x 2 x 2 x 2 + 2 = 18,
so I'm not sure why you'd complain about the damage at all.