Why is it bad if, say, the NPCs have a few more or less skill points or feats? As I said before, such discrepancies could also be the result of a higher int, or higher level, and I doubt anyone of us would expect the DM to use strictly by the book NPCs, and never play around with the stats. If I can accept that there may be orcs with higher Int than the average orc in the MM, why should some minor discrepancies between PCs and NPCs be ground to worry?
Again, why would it be a problem if the NPC bard the PCs encounter has not 6 skill points per level, but only 4? (Apart from the fact that the DM could easily rise his int by 4 to compensate, if he feels it warranted, or skip lowering the bards int.)