Are size bonuses / penalties always the same, regardless of source?

Size bonuses and penalties are mentioned in numerous places throughout the rules. The Small races (Halflings, gnomes, etc) get +1 size bonuses to AC and attack rolls, a -1 penalty to CMB and CMD, and a +4 size bonus on Stealth checks. A spell such as Enlarge/Reduce Person grants size bonuses/penalties to attack rolls and AC, but do not mention Stealth checks. (The CMB/CMD adjustments aren't mentioned explicitly, but the rules for those stats account for size specifically already).

My question is: does every size category carry with it some sort of "absolute" bonuses and penalties, regardless of how the creature came to be that size? A halfling who has Enlarge Person cast upon them will have their size bonuses and penalties to AC, attack rolls, and CMB/CMD "canceled" by those granted by the spell, leaving with +0 to everything (the same as a medium creature would have naturally). Would that still be true if they were to become Medium size by virtue of the Best Shape 1 spell? It makes no mention of size bonuses to attack rolls/armor class. Likewise, there is no mention of the Size bonus to Stealth checks in any of these other sources; would a Halfling polymorphed into a Huge creature still receive a +4 Size bonus on Stealth checks?

If anyone has any links to specific rules entries I could reference for this, it would be appreciated. I'm trying to write a spreadsheet function that accounts for the mechanical effects of changes in size, but the specific effects don't appear to be consistent; ie, being "Small" from a polymorph doesn't necessarily have the same mechanical effects as being "Small" naturally as a Halfling, or from casting Beast Shape I, etc.

TLDR: I am trying to figure out if bonuses from Size are absolute (ie, a Small creature always gets a +1 size bonus to AC/etc) or relative (ie, a Small creature may get a +1 size bonus to AC if they are Small because of being a Halfling, but not if they are Small from casting Beast Shape I)

They are always the same.

In other words all small creatures will have the same penalty/bonus, as an example no matter how they came to be small.

From the Polymorph school description:

"If a polymorph spell causes you to change size, apply the size modifiers appropriately, changing your armor class, attack bonus, Combat Maneuver Bonus, and Stealth skill modifiers. Your ability scores are not modified by this change unless noted by the spell."

If you need to know what there penalties/bonuses are, there is a table in step 2 of the Monster Creation rules. Also, if you ever use a polymorph spell to alter the size of a creature other than Small or Medium, there is a table under the Polymorph school that tells you how to adjust their scores. If there size is adjusted some other way, such as natural growth, there is a table under step 2 of monster creation that tells how to adjust ability scores.

In other words, all benefits from being a size other than base stat adjustments are the same regardless of how you got that size. Stats change depending on the method.

From the responses here I went digging further into things and discovered that, indeed, the size modifiers are absolute. They are just not presented in an obvious way:

• Size modifiers are listed as part of the attack roll and armor formulas, referencing the values in this table.

• Size modifiers are listed as part of the CMB and CMD formulas, with a specific list of values to use provided in that section (not as a table).

• Size modifiers to Stealth are listed in the "Check" section of the Stealth Skill Description.
  

The fact that some of the effects which change Size repeat some (but not all) of these modifiers is where my confusion stemmed from. Ah well- glad to get to the bottom of things!

The modifiers mentioned in the first paragraph are automatic consequences of being Small and Seidaku's last post makes an excellent point in support of this.

Some other changes applied by different means of changing size - notably, to ability scores, natural armour and reach - are not standardised or automatic, particularly when magic is involved.

What about the spell Form of the Dragon?

I: Become medium, +4 size bonus to strength, +2 size bonus to constitution

II: Become large, +6 size bonus to strength, +4 size bonus to constitution

III: Become huge, +10 size bonus to strength, +8 size bonus to constitution

I thought that this meant whether you are a halfling or a human, you always get the listed size benefits (and no dex penalty) in place of the default size bonus for your new size category.