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You will start with 34 ability power but is it worth it?
some math:
LvL 1 Disintegrate with all flat AP runes:
90 base + 25.5<<(.75 ability scaling *35 AP) *.76<<(100/100+30 equation for damage multiplier for 30mr)
= 87.78 true damage to a Champion at lvl 1
LvL 1 Disintegrate with 8.55 Magic Penetration from Mrp Marks
90 base + 22.26<<(.75 ability scaling * 29.69 AP) * .823<<(100/100+30-8.55 equation for damage multiplier for 30-8.55)
= 92.38 true damage to a Champion at lvl 1.
Big woop, its a 5 damage increase... But the beauty of Magic Penetration is it scales with all magic damage including items and the base damage of your abilities and any bonus damage from the AP as long as you don't surpass your opponents Magic Resistance. This alone would give you reason to run Mrp marks with any hero who deals magic damage(unless they used healing which isn't reduced by allied magic resist, or had some scaling above 1.0).
If your worried about last hitting minions who would initially take the extra damage-- I can't really see the justification as Annie is really easy for last hitting and getting cooldown reduction would be better for last hitting with Disintegrate more often.