Wands and Rods are actually quite distinct, not just for the reasons that you mention (which are great indicators that "higher level wands just do the same thing as rods" is malarkey)
After all, stuff like Dual Wand Wielder, Wand Master, Wand Modulation, that Warforged feat that let's you cast spells off wands as if they were runestaves, and a few other options that I forget about apply just to Wands, not to Rods.
After all, the higher-level version of Wands are Sceptres, which have one spell of up to 7th level and another spell of up to 4th level in them, both of which pull from the same pool of charges.
Hell, you might as well change the rules so that Staves count as wands for the purposes of your class features.
Or, as just a quick thought, add some method to use Eternal Wands as wands for the purposes of class features; that would be sweet!