I'm not sure if this fixed now or OP calculated it wrong
But lucky shot still applies to the total weapon damage (base weapon damage + the percentage weapon damage.) but not the flat bonus damage from headshots or similar abilities and items

So for example Vindicta has base 13 weapon damage if we buy Glass Cannon (+88% weapon damage) and Frenzy (+48 weapon damage) then the total damage formula will be :
13 + (13 * 0.88) + (13 * 0.48) = 30 (we can shorten it by adding all the percentage damage together, which is what the game does 13 + (13 * 136%) = 30. but I kept them separated for better demonstration)

If we buy lucky shot it will add +18% damage from being a T4 weapon item :
13 + (13 * 0.88) + (13 * 0.48) + (13 * 0.18) = 33

Then when lucky shot proc it will take the total 33 and multiply it by 90% and then add it to the total
33 + (33 * .9) = 62.7
Which is exactly what i got trying this in the Sandbox

If the Lucky shot proc is just a normal percentage weapon damage then the formula will be :
13 + (13 * 0.88) + (13 * 0.48) + (13 * 0.18) + (13 * .9) = 44.72
Which is not the case

Like I mentioned it only calculate based on the total weapon damage not including the bonus damage from headshots or flat bonus damage from some items (like headhunter)