Ok, so the passage you originally quoted doesn't make too much sense when you actually apply it across the content of the game. There's a lot of those in the Infinity rules, probably down to poor editing.
I wouldn't say so. A "bonus" given to me as part of my pay is additional to my existing pay scale; "your pay is now 100k for this year" is not a bonus.
Is the arguement still going? In the Reactive Turn, this +1 Burst bonus is not stackable with other bonuses or Burst MODs provided by other rules, Special Skills, Equipment, or Hacking Programs, except for those who specifically state otherwise So, not stackable with Hacking Programs. There are, to my knowledge, only 2 Hacking Programs that affect Burst, both of which have basically same wordings, especially in the area of "...except for those who specifically state otherwise."