[RPG] Do penalty modifiers in ranged combat really stack

Yes, and no.

When making a melee attack against a target that isn't adjacent to you (such as with a reach weapon), use the rules for determining cover from ranged attacks.

This means that if you are attacking an opponent on the other side of a low wall, another creature, or anything that would normally be treated as cover if you were shooting/throwing a weapon at said opponent. However if there is nothing between you and the target's square that would generate cover then there is no penalty. You can flank with reach weapons without penalty.

To determine whether your target has cover from your ranged attack, choose a corner of your square. If any line from this corner to any corner of the target's square passes through a square or border that blocks line of effect or provides cover, or through a square occupied by a creature, the target has cover

In addition, the only penalty for using a reach weapon into melee(due to it being treated as a 'Ranged' attack) is that of the cover penalty. There is no need for Precise shot.

Yes, ranged attacks from spells are typically considered to be "weapon-like". This is definitely true of rays (and almost all ranged touch attack spells are rays) since from the rules:

You aim a ray as if using a ranged weapon

The rules further clarify that rays function as weapons for several other purposes, and the FAQ makes this very explicit:

Do rays count as weapons for the purpose of spells and effects that affect weapons?

Yes [...] rays are treated as weapons, whether they're from spells, a monster ability, a class ability, or some other source

The same rule applies to weapon-like spells such as flame blade, mage's sword, and spiritual weapon--effects that affect weapons work on these spells.

Most ranged touch attacks which aren't rays are things like acid splash -- spells where you actually throw or aim a physical object. Those are even more "weapon-like" than rays, so it's probably simplest to say all ranged touch attacks work like this.

There's another FAQ that indicates you can take "Weapon Focus (ray)" and the like; strictly speaking I guess those wouldn't apply to orb spells like acid splash.

This is all following the precedent set by 3.5; in Complete Arcane it specifies that rays and touch attack spells are "weapon-like" and thus interact with feats in the same way that other weapons do, with a split between ranged/melee type spells.