In 3.5, when you wanted to improve a monster with a template or adding Hit Dice, you could also change the standard ability array and use instead elite or non-elite ones. In Pathfinder, I've noticed that only when you add pc-classes or npc-classes to a monster you can use these (elite for pc, nonelite for npc). Is this correct? So monsters that advance solely using templates or adding hit dice always use standard array of abilities?
By the rules you have to apply a template, add HD, or add class levels which improves the stats, and you start with the base stats from the book.
As GM you can change whatever you like. Nothing to stop you changing the stats of a monster up or down as you see fit. The only issue is that there are no clear guidelines for what effect this will have on the CR.