The word include indicates a subset: every element that is included appears in the including set.
So the statement about the cloistered cleric’s class skills is that the given list, “Decipher Script, Speak Language, and all Knowledge skills (from the Knowledge domain, see below),” is a subset of the full set cloistered cleric class skills. This explicitly does not tell us whether or not this is the complete list: the word includes means that these skills definitely are present, but does not say whether or not anything else is also present.
However, the statement that the class operates as normal for that class unless otherwise specified does tell us about the complete skill set: it also includes the original cleric skill list.
So the complete list must include both the original cleric skill list, as well as the specifically named skills. They are, in effect, added. Which is consistent with the description of how skills may be changed: variants may list “Additions or subtractions from the class skill list,” but the rules do not allow for the possibility of outright replacement. Only additions and subtractions are allowed. Since nothing in the cloistered cleric description explicitly subtracts any of the original cleric class skills, the cloistered cleric has each as a class skill.
Would it have been clearer if they’d just said “add”? Yes. I don’t know why they didn’t. But despite the lack of clarity here, the rules still amount to the same thing.
TL;DR: Cloistered clerics have all the cleric class skills, plus a few more
No.
A race defined by class levels with a racial bonus in a skill does not automatically treat it as a class skill. The rules text quoted in the question has been taken out of context and does not apply to PC character creation.
The text referenced in the Monster Manual is written in the context of building and reading monster statblocks. The Skills heading of Reading the Monster Entries not only clarifies this, but also says that having class levels exempts a monster from receiving these free class skills.
Skills
This line gives the creature’s skills, along with each skill’s
modifier (including adjustments for ability scores, armor check
penalties, and any bonuses from feats or racial traits). All listed
skills are class skills, unless the creature has a character class
(noted in the entry). A creature’s type and Intelligence score
determine the number of skill points it has. (7)
The text quoted on page 307 is a further elaboration on the above text from page 7 meant to explain how to interpret and rebuild a monster's statistics. It mentions skill ranks and racial bonuses because a skill is usually only listed in a monster's entry if that monster has a rank or a racial bonus to that skill. Indeed, the Glossary entry on class skills goes on to explain when you should interpret a skill listing as a class skill or whether the skill is listed simply because it's relevant to the monster's special abilities. This text has nothing to do with PC character creation, and should not be taken out of context to apply to how to build PC characters.
Not only has the text been taken out of context, but also you can easily see plenty of evidence that proves contrary to what this question suggests. For example, there exist numerous examples of NPCs that do not receive free class skills just for having a race with bonuses on skill checks. Some PC races explicitly give class skills as a racial trait.
Best Answer
You have a few misunderstandings, which explains the discrepancies that you see.
To begin, Seoni does not have the ranks you think she has. The bonuses listed for her account for all bonuses to those skills, not just ranks. Namely, her lizard familiar gives +3 to Climb, which accounts for the entirety of the +3 bonus listed for her, so she has zero ranks in that.
In addition, Alertness adds +2 to Perception and Sense Motive, and World Traveler adds +1 to Diplomacy, Knowledge (local), or Sense Motive and makes the chosen skill a class skill. These are both Wisdom skills, so +1 for 13 in that, for +3 Perception and +4 Sense Motive. So zero ranks in these skills, too. Note that Sense Motive is a class skill for her, thanks to World Traveler, but she doesn’t get the +3 because she doesn’t have the 1 rank.
Furthermore, human racial traits include an extra 1 skill point per level, so that brings Seoni to 3. And anyone may choose to get +1 skill point per level when taking a level in their favored class,1 which would bring her to 4, but Seoni has instead elected to take the +1 HP (hence her 1d6+2 with only Con 12).2
Finally, Seoni’s arcane bloodline adds any one Knowledge skill as a class skill. In this case, Seoni’s choice was Knowledge (planes), and that explains the +4 bonus.
Thus, Seoni has 3 skill points (two from sorcerer, one from human), in Bluff, Knowledge (planes), and Spellcraft.
Humans may have any one class as their favored class; for Seoni, that’s clearly sorcerer.
Other options are defined for a particular race/class combination, such as the “Add one spell known from the sorcerer spell list. This spell must be at least one level below the highest spell level the sorcerer can cast” option added by Advanced Player’s Guide for human sorcerers. But the 1 HP or the 1 skill point are always options.
As a complete aside, everything figuring all of that stuff above was hard—I originally couldn’t account for the Perception and Sense Motive bonuses because I forgot Seoni had Wisdom 13 (thanks to @user28605’s answer for pointing it out). And I have an awful lot of familiarity with these rules.
Ultimately, the iconic characters are meant to just be played, as is, often by the GM as an NPC. They aren’t really useful for trying to understand the game, because they don’t break down which bonuses come from where. Even playing as Seoni would get quite difficult the moment she levels up, since then you would need to know about her skill ranks.
So I would suggest that trying to understand a completed character’s final stats and reverse-engineer where all of the bonuses came from is a very difficult, time-intensive process. If you are new to the game, it probably isn’t worth trying to do it.