To quote the SRD, "In addition, certain spells and effects function differently against the creature, as noted below." Emphasis mine.
Differently does not mean "the same as normal". Differently does not mean "the same but with extras". Differently means DIFFERENT. The particular effects noted in the golems' descriptions have DIFFERENT effects on them, not the normal effects.
They do not deal damage normally or whatnot, they just have the specific effect mentioned in the golem's description. Because DIFFERENT does not mean THE SAME.
If the designers were saying that certain effects worked on the golems with extra side-effects, then they would have worded it as "In addition, certain spells and effects function normally against the creature and ignore its Immunity to Magic, with additional effects as noted below".
They did not. They said only that the effects work differently against golems, and differently means that they don't have the normal effects.
The "otherwise" clause in some of the golem descriptions, like here "Any magical attack against a clay golem that deals acid damage heals 1 point of damage for every 3 points of damage it would otherwise deal.", just means that they're describing the fact that the particular kind of damage is converted into healing or something else, since of course, healing isn't normally inflicted as damage, and damage doesn't normally cause healing.
The designers didn't leave it unclear. The wording is clear on what it means, that certain magic has different effects on golems rather than the normal effects. The only thing they didn't make clear in 3.5 was whether or not spells that normally allow SR would bypass their Immunity to Magic, because the designers worded that first line poorly.
This wasn't even an issue in 3.0 rules, because it wasn't until 3.5 that they went and changed the wording to mention Spell Resistance as a qualifier; in 3.0, golems were just immune to all spells, spell-like effects, and supernatural effects, except for the specific few effects listed as exceptions. SR didn't matter; the specific effects mentioned in their descriptions just bypassed their magic immunity altogether and had their different effects on the golems, but there was no confusion over it.
It was the stupid 3.5 design change that messed up a perfectly clear wording in the first line of golems' Immunity to Magic.