[RPG] How to calculate scores for skills?

A +29 on Intimidate is a very large bonus. Especially on a fighter, who has few skill points and little use for Charisma in most cases; almost all of that is probably from skill ranks, which implies a very high level character.

Such a person should be trivially succeeding on attempts to demoralize most anything. Anything short of an actual god should be an easy target for this guy’s demoralizing. He’s that good. Demons quake and angels shudder before his fearsome gaze. And so on.

The DC to use Intimidate is not based on the chart you gave, however; see the entry for the Intimidate skill on PFSRD:

Demoralize

[...] The DC of this check is equal to 10 + the target’s Hit Dice + the target’s Wisdom modifier.

Influence Attitude

[...] The DC of this check is equal to 10 + the target’s Hit Dice + the target’s Wisdom modifier.

So you can see that the DC scales with the target you are facing. Assuming the fighter’s Charisma is the same as the target’s Wisdom, and they are the same level, and neither has any relevant special bonuses, his average roll is only 3 higher than the target’s DC (from the +3 for Intimidate being a class skill). That gives him a 65% chance of success; good, but certainly not great.

If the target is higher in level, or Wisdom relative to his Charisma, or has other bonuses, that 65% chance quickly becomes 50:50 or worse, which makes even trying to intimidate a fairly risky move (in combat, it wastes time that could be spent attacking, out of combat, it pisses the target off).

But since the fighter is high-level, or has an unusually high Charisma and/or sizable extra bonuses, he’s basically guaranteed to terrify lower-leveled characters. This is a good thing; it represents his training, prowess, and so on. The table you give that ignores the player's bonus completely defeats the purpose of having that bonus, which is really bad for the game: it means the character's training and Charisma and other bonuses are meaningless.

As for Disable Device, for mundane traps it has more static DCs that don't necessarily scale. This is fairly appropriate; there's a limit on how complex a machine is reasonable in the kinds of gameworlds typically seen in Pathfinder. In an unusual setting, you could imagine more complicated machinery that requires higher checks and/or specialized training. Even within Pathfinder, an Amazing lock has a DC of 40, which is very difficult even for high-level characters to make.

Plus magic traps have scaling based on the spell level used to make it, and only those with Trapfinding can even try to make the check.

But again, many checks are going to be very easy for high-level characters. This is intentional. They are high-level; they are supposed to be good at what they do. In a lot of cases, they really aren’t that good at what they do; using magic tends to work much better than using a skill.

Those numbers are your overall modifier for that skill or saving throw. They include your proficiency bonus if you are proficient in them, otherwise they are just your ability modifier for that skill or saving throw. They're pre-calculated and listed on the sheet for convenience during the game so that you don't have to add up all your modifiers and Proficiency bonus every time that roll is made.

So if your example Cleric is proficient in Wisdom saving throws and has a Wisdom score of 15, their Wisdom saving throw modifier = proficiency bonus (+2) + Wisdom modifier (+2) = +4, which is the number that will be listed under Wisdom saving throws.

On the other hand, your Cleric probably doesn't have proficiency with Dexterity saving throws, and let's say their Dexterity score is 8. Their Dexterity saving throw modifier = no proficiency bonus (+0) + Dexterity modifier (-1) = -1.

There are other factors that can affect this calculation, such as the Rogue's Expertise feature, but this is the basic calculation that will be used in the vast majority of cases.