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Well, i have done a few calculations related to armor penetration and flat attack damage runes.
Here is what i did in calculation
Armor works something like this
(X/X+100)*100 with X being the armor
as we are talking about armor penetration and attack damage, it would be 8 damage versus 12 armor penetration with tier 3 marks
at 100 armor, you will do 4% more damage with 12 armor penetration
for that 4% to = 8 or at a equalibrium point you will need 200 damage. only at 200 damage and above armor penetration will than deal greater damage than flat attack damage runes with the enemy having 100 armor.
at 50 armor, you will do 6% more damage with 12 armor penetration
for that 6% to = 8 you would need 133 or 133
at 25 armor you will do 8.5% more damage with 12 armor penetration
for that 8.5% to be = 8 you will need 94 damage.
at 12 armor you will do 11% more damage with 12 armor penetration
for that 11% you will need 75 damage.
Generally speaking, people will have armor seal of some kind in both the bottom lane or the top lane. In my opinion alot of adc top lane and support start with around 25 armor at level 1, so to really to have all the benefit from armor penetration at level 1, you need to have a physical damage skill which can do at least 94+ damage( i doubt that flat attack would get up to 94 at level 1). Armor penetration dont really do alot in the early games tbh, as most champion simply cannot do 94+ damage with level 1 skills. It really shines when you start to do massive damage only till than will you actually out do the 8 flat attack damage rune.