I did think I remember it being said that any "bonus" damage of abilities (damage applied over the initial damage percent of an ability) did not correctly apply attack percentages. That may have been fixed, however.
There are times I try to test damage numbers, but I fail miserably. I'll calculate that <insert ability> will do <insert damage> based upon <insert variables> using the known damage formula. Then I get in game and the numbers I see are way off what I calculated, and I can never figure out why. Like when I calculated that my critical hits with a fully triggered Long Shot should be like 2k damage, and in came it came out to like 3.5k damage. 1,500 damage is quite a mathematical error, if you ask me lol.
As a result, I stab at theoretical damage calculations, but never invest too heavily into them. I think that BioWare knows when I do, and trolls me for lawlz.
I know what you mean, usually I find it's best just to go in game, hit something, then use a power, then work backwards against the formula the power is meant to use. The other problem is sometimes it's difficult to determine what the "bonus" damage is meant to be when you look at a tooltip:
Say a theoretical ability that does 200% damage, + 300% vs disabled targets, with an upgrade that's a 400% bonus... is that 600% + 300% when upgraded, or 200+700? or 200+400 (400 replaces 300)? Only by hitting things and "reverse engineering" the results can we be sure.
Armor, resistances and passives throw things out too - does armor affect the extra damage from the rune for a physical damage ability, does resistance or vulerability affect it?
Does armor apply only "once"?
For example, with a physical damage ability that's 400% weapon damage is armor before, or after the 400%?
Is it:
200 weapon damage - 30 armor = 170 with +60% attack = 272 times 400% for an ability = 1088 damage
Instead of going:
200 weapon damage times 400% for a power = 800 damage - 30 armor = 770 with +60% attack = 1232 damage
That's almost a 15% difference (in this particular example), make it a crit and it jumps to around 20% difference (or more if you've got + crit damage %)
I'm pretty sure it's applied after, which usually gets my "theoretical numbers" close to what I see in game when I test, but often when just bandying numbers around I don't bother thinking too hard about where armor may come in.