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You seem to be right, the size bonus and size penalty to attack rolls apply only for specific things, such as being a gnome, halfling, goblin, kobold, ratfolk, grippli, svirfneblin, or wayang; or spells such as enlarge person or reduce person. Are these only applicable then for these specific circumstances? So a Goblin PC would get a size modifier and size bonus on attack rolls?

By your definition you would have to include both.

Bonus: Bonuses are numerical values that are added to checks and statistical scores. Most bonuses have a type, and as a general rule, bonuses of the same type are not cumulative (do not “stack”)—only the greater bonus granted applies.

Penalty: Penalties are numerical values that are subtracted from a check or statistical score. Penalties do not have a type and most penalties stack with one another.

Determine Bonuses... A positive modifier is called a bonus, and a negative modifier is called a penalty.

Funny thing: the playable races all have a untyped modifier to CMB+CMD and the modifier to attack rolls is specifically typed as "size" and therefore would not stack with another size modifier when rolling attacks.

I still follow " you shold not apply a modifier from the same source twice" which is consistent through all rulings and therefore replace the size modifier to attacks/attack rolls with the size modifier to cmb/cmd when making an Combat Maneuver check

Nope both are a size modifier

Edit : where exactly did you find the penalty to attack rolls ?(some spells have it ,Esp. Enlarge person which has its own rules of you get what is written but i could not find it with this wording in the combat or creature sections of the prd (I only have a tablet at hand))

You cannot include a modifier twice You already applied a size modifier (CMB) which specifically replaced the size modifier to attacks from the attack bonus.

Do you apply the attack modifier twice when making a melee attack? No, because it is incorporated in the base formula for the attack bonus. Same here.

As I said above, I want to see this "leap." I only have access to the rules, not implied logic.

There is no leap.

The size modifier to attacks is part of the attack bonus . (combat chapter core rulebook)

The CMB includes the size modifier to combat maneuver rolls.

When you roll an combat maneuver you replace the attack bonus with your CMB. The size modifier to attacks is part of the attack bonus and therefore no longer part of the combat maneuver roll.

Just look at the exact formulas and what replaces what. Its all in the core rules.

@veldebrand: for secondary attacks there is no -5 to attack rolls,there is a -5 to the used bab. This is important when you look at the attack bonus and CMB formula. The -5 affects the attack bonus (bab + str mod+ size mod) in modifying the bab with -5. The rest of the logic is the same: the attack bonus is replaced by the CMB.the CMB has no rules for secondary attacks so it uses the full bab.

All other modifiers (apart from bab,str and size) are not included in the attack bonus and CMB formulas and are applied after replacing attack bonus with CMB.

The -2 for size certainly does not apply. If it did apply in this instance, it would always apply, and so would be figured into the CMB.

This is correct, look at the PRD:

Attack Bonus

Your attack bonus with a melee weapon is the following:
Base attack bonus + Strength modifier + size modifier

CMB = Base attack bonus + Strength modifier + special size modifier

Size mod for attacks is -2.

CMB replaces Attack Bonus in this case so no -2.

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Following is open to debate:

Secondary attacks are made using the creature's base attack bonus –5

So the -5 applies to the Creatures BAB for secondary attacks. So for secondary attacks the creatures BAB is treated as BAB-5. This should not apply for the CMB check because the CMB replaces the Attack Bonus and BAB changes are part of the Attack Bonus and not applied later for secondary attacks.

... I say this because it doesn't explicitly state in the section on diseases that these saving throws, like regular ones, autopass on a 1 and autofail on a 20, and in my warped view of specific trumping general, I believe lack of specific reiterating general trumps general. Plus, it's possible to be immune to disease, so it makes sense that a 1 shouldn't be an automatic fail.

The RAW is ambiguous. Teach the controversy.

so you are saying that Touch Attacks should not autohit on a 20 or automiss on a 1 because it is not specifically reiterated in the touch attack section?

Touch Attacks: Some attacks completely disregard armor, including shields and natural armor—the aggressor need only touch a foe for such an attack to take full effect. In these cases, the attacker makes a touch attack roll (either ranged or melee). When you are the target of a touch attack, your AC doesn't include any armor bonus, shield bonus, or natural armor bonus. All other modifiers, such as your size modifier, Dexterity modifier, and deflection bonus (if any) apply normally. Some creatures have the ability to make incorporeal touch attacks. These attacks bypass solid objects, such as armor and shields, by passing through them. Incorporeal touch attacks work similarly to normal touch attacks except that they also ignore cover bonuses. Incorporeal touch attacks do not ignore armor bonuses granted by force effects, such as mage armor and bracers of armor.

In order to confirm a crit you must hit the target's AC, something a natural 20 doesn't always do.

A natural 20 (the d20 comes up 20) is always a hit.

A 20 is a hit.