I don't reduce stress boxes for sub-mediocre skills. And I do use them all the time - for an ordinary person, there are plenty of skills that *default* to -2. For example, survival, weapons, lore, guns, burglary... All of these are things that, for an example, I personally just can't do unless I get really lucky, or have a lot of time to do the research and set things up (i.e. take extra time on several preparatory maneuvers.)
I treat a skill value of +0 as being mediocre... for someone who actually makes common use of that skill. Thus, PCs defaulting to +0 on skills is something that makes them *special*, a cut above the normal human.
I wouldn't give any rebates, though. And keep in mind, the pyramid is a PC-only thing; the only times I use it for NPCs are when I know that NPC is likely to "join the party" so to speak, and thus needs to be balanced against the PCs for relatively long term use. (Or, ok, when I'm just having fun statting up a character for my own entertainment.)
If anything, just move the base of the pyramid up or down; if someone starts with -2 everywhere, then buying up to -1 costs them a skill point, and their peak skill is likely to be +1 or +2 at the most. Which, hey look at that, fits right in with the book's notion on what an NPCs skill in the-thing-they-do-for-a-living ought to be - +1 up to maybe +3 for particularly good musicians / programmers / truck drivers / whatevers.