Mathematically percentage roll under and d20 add modifiers are identical. The only time it matters is when you have modifiers smaller than 5 percent, but generally these would be so insignificent they are unlikely to actually matter in play.
Personally when I created Heart of Darkness I started out dong percentile roll under, but switched to d20 plus modifier. I find it is much faster and more intuitive, particularly if you need to roll multiple dice at one. For example, if I have five mooks shooting at the PCs I can just grab 5d20 and roll them. That is much easier than finding 10d10, sorting them into pairs, and distinguishing the tens digit and the ones digit.