I hadn't even considered using the two bonus actions for attacks... (I switched in a rapier early on)... I don't understand this, weird rogue situation at all. Sneak attack only works on main hand attack, then you can off hand attack twice but can't use either of them for sneak attack?
I understand a 1 to 1 translation of tabletop to game isn't always possible, but this seems like they made this aspect way more complicated than it needs to be.
Frankly sneak attack should apply automatically if any of the criteria is met (maybe a pop up to show you got your sneak attack damage), whether it is an attack action or a bonus attack.
Letting rogues attack three times because of the extra bonus action should not be happening at all, make it a once per turn function.