I think the rules for Bonus Damage are worded a bit ambiguous. I can't quite tell if you do an additional damage roll or just adjust the regular damage roll.
The idea is probably to adjust the regular damage roll, but in that case you're not so much dealing "bonus" damage as much as you get a higher chance of dealing max damage - except when the base damage is Fray only, in which case you do get to add an entire damage die.
It is also not spelled out how multiple instances of Bonus Damage stack. RAI seems to suggest you roll more dice, but don't get to keep more.