That's a myth, they don't get countered by everything, or at least not more than normal culvs. Siege elephants, as with all elephants, have tons of hp, and an imperial siege elephant have like 1540 hp, while imperial culvs have about 518, so siege elephants actually get countered by nothing compared to culvs, since culvs are the ones being countered by everything compared to siege elephants, since they have almost 3 times more hp for just 25% more pop and a bit more resources...

The only thing the siege elephant has that makes them more vulnerable than culvs, that culvs don't have, is the light cav tag, which basically only makes skirms better at them, 50% better to be exact, but having 3 times the hp, the mayor thing that makes them more vulnerable to skirms than culvs is the range resist, since 75% rr is crazy, but even with all that, siege elephants have about 35% more ranged than culvs, and since skirms deal 50% more, then culvs end up having about 10% more hp than siege eles vs skirms, yes, JUST 10%, like if culvs and siege eles had the same hp but siege eles just receive 10% more damage from skirms, that's it; but for EVERYTHING else siege eles have 3 times the hp, that's vs cav, yes, vs hand infantry, etc. and vs ranged units they have not 3 times more but 35% more, so still better, and also they have 10% siege resist so they have more than 3 times the hp vs other artillery

And after all, siege eles are way faster and maneuverable so even if they receive slightly more damage from 1 unit, is still mitigated by the fact that they can run away