[RPG] Are ghost touch weapons the only way to bypass the 50% chance to ignore damage against or by incorporeal creatures

The weapon special ability ghost touch doesn't allow the wielder to make incorporeal touch attacks

That last sentence isn't the extent of the description. In its entirety, the weapon special ability ghost touch says

A ghost touch weapon deals damage normally against incorporeal creatures, regardless of its bonus. (An incorporeal creature’s 50% chance to avoid damage does not apply to attacks with ghost touch weapons.) The weapon can be picked up and moved by an incorporeal creature at any time. A manifesting ghost can wield the weapon against corporeal foes. Essentially, a ghost touch weapon counts as either corporeal or incorporeal at any given time, whichever is more beneficial to the wielder. (DMG 224-5)

When the text says, "Essentially, a ghost touch weapon counts as either corporeal or incorporeal at any given time, whichever is more beneficial to the wielder," the text is clarifying, providing the reader with a summary of the weapon's fundamental functions that have already been described. It means the weapon strikes foes despite their corporeal states and the wielder can continue to use the weapon despite the wielder's corporeal state. Nothing more.

As you've noted, taking that last sentence out of context makes the weapon special ability ghost touch way more powerful than it should be for its +1 bonus.

The weapon by that sentence isn't given additional properties beyond what's already been described.

The MM and DMG agree that an incorporeal creature's physical attacks (whether with a ghost touch weapon or not) ignore non-ghost touch or non-force material armor

In addition to the Monster Manual's description of the subtype incorporeal (310-1), the Dungeon Master's Guide on Incorporeality says that

The physical attacks of incorporeal creatures ignore material armor, even magic armor, unless it is made of force (such as mage armor or bracers of armor) or has the ghost touch ability. (DMG 295)

So, while it's a little weird that a ghost (or an unbodied) can pick up from the floor a +1 ghost touch longsword and, bypassing the dude's full plate, stab the dude to death with that sword, that appears to be how it works. But were that sword not to have the weapon special ability ghost touch, the ghost would just look at the sword on the floor with despair. Okay, even more despair ('cause it's a ghost).

A magic weapon has an enhancement bonus; the size of the bonus is listed in the name of the weapon (a +1 short sword has a +1 enhancement bonus, a +2 short sword has a +2 enhancement bonus, and so on). Specifically, this is an enhancement bonus to the attack rolls and damage rolls made with that weapon.

A bonus is just a number that you add onto another roll. The “enhancement” term indicates the type of the bonus; the only significance of the type is that bonuses of the same type don’t stack. For example, a +2 short sword must also be a masterwork short sword (since all magic weapons must be masterwork). Masterwork gives a +1 enhancement bonus to attack rolls (not to damage rolls), but since this is also an enhancement bonus, attack rolls with the weapon only get the higher of the +2 enhancement bonus from its magic and the +1 enhancement bonus from its being masterwork, that is, you only add +2 to your attack rolls when you swing it.

The enhancement bonus to damage rolls works the same way: it adds on to the existing roll. A +2 short sword adds +2 to the damage roll. This is added on to the weapon’s damage die (1d6, assuming a Medium short sword), as well as any other appropriate bonuses (e.g. the wielder’s Strength bonus). Again, it would not stack with any other enhancement bonuses to the damage roll, for example from a magic weapon spell cast upon the sword.

It doesn’t actually change the damage type at all; it is just adding a certain amount to the piercing damage that the short sword deals. “Magic damage” as such is not really a thing.

What you are thinking of is the ability to penetrate damage reduction listed as “DR X/magic,” or perhaps “DR X/magic-and-piercing,” as well as the ability to attack incorporeal creatures. The entire 1d6+2 (or more, from Strength or other bonuses) penetrates these sorts of damage reduction and can attack incoporeal foes, because the rules for damage reduction (D&D 3.5, Pathfinder) say:

Some monsters are vulnerable to magic weapons. Any weapon with at least a +1 magical enhancement bonus on attack and damage rolls overcomes the damage reduction of these monsters.

And the rules for incorporeal (D&D 3.5, Pathfinder) state:

Incorporeal creatures can be harmed only [...] by magic weapons [...] Even when struck by magic or magic weapons, an incorporeal creature has a 50% chance to ignore any damage from a corporeal source—except for a force effect or damage dealt by a ghost touch weapon.

Here you can see that it isn’t that the magic weapon changes the type of damage dealt, it’s that the damage reduction and incorporeal properties themselves specify that if the weapon is magic (has at least a +1 enhancement bonus), the entire damage roll ignores the DR or incorporeality.

So when people, or even the rules, talk about “magic damage” or “magic piercing damage,” they’re really using a shorthand: the damage is “damage, that is being dealt by a magic weapon” or “piercing damage, that is being dealt by a magic weapon.”

The types of damage are bludgeoning, piercing, or slashing (collectively, “physical” damage, affected by damage reduction), acid, cold, electricity, fire, or sonic (collectively, “energy” damage, affected by energy resistance), and then more exotic things like force damage (magic missile, automatically hits incorporeal targets and generally exempt from resistance or immunity), untyped damage (the Complete Arcane warlock’s eldritch blast, also generally irresistible), vile damage (various effects in Book of Vile Darkness, cannot be healed), dessication damage (some effects in Sandstorm, can cause fatigue), and so on. The City Magic feat from Cityscape wins for the bizarrest entry here: it converts half a spell’s damage to “city” damage.