Heh, interesting. Looking at it again, I figured out why I thought that it is a bug. As per the rules I it is not a bug.
The "bug" is actually a side effect to two parts of my house rules:
1) Attribute maximums are based on any Race Attribute mods, so a race (like the Dwarf) with a Vigor d6 base can have up to a d12+1 Vigor.
2) Skill maximums are based on Rank, so a Novice can have a d8 in a skill. This increases for Race mods, so a race with a d6 skill can have a d10 at Novice.
The effect that having the bonus to the trtRoll on an attribute or skill is that it is applied as it is calculated, and the bonus is overwritten by the attribute or skill the 7th pip increase (when d12 becomes d12+1). This does not happen normally because the trtMaximum is not normally a dynamic variable.
I am sorry that I announced that as a bug. However if you think about it, the bonus
should be applied after the Trait value is first determined. Pre-Traits should determine the base value, then Traits (after it is fully defined) applies the bonus/penalty on top of it. This is when other things in the code apply mods, and a bonus to a skill (on top of its rank value) is conceptually the same thing. An example of this that happens offhand is when the melee weapon makes its value be the strength value if the person is too weak. That is technically a "penalty".

In fact, that is when I applied one for being weak (I gave Fighting the same penalty to hit that Ranged weapons have from being weak).
I think that the Supers attributes and skills are also likely to be static, but if they are dynamic like my house rules above they will run into the same problem (which is fixed by changing it to Traits).
For some reason it does not work all that well when applied as part of Final. I suspect that it is because it collides with the official scripts (as per the source code) which do often happen at that timing.