Like I said before, Spells are made by people, they don't come from nothingness. Also I don't know about your entire list, are the ones that start with Vivec created by Vivec or just named after him? Anyway sure most of these mages created these spells.
However, I'm pretty sure they didn't do it by standing in front of a glorified music stand and pouring literally tons of gold into it somehow (assuming 1 septim is 1 ounce of gold)
Gameplay mechanism, yes an actual npc you interacted with to create the spell like in Daggerfall and Morrowind feels better, this trained mage help you put together the spell so it have the wanted effect, you could actually make this totally dialogue based but it would be less user friendly.
Enchanting makes more sense using some sort of device, an npc would here only operate the device for you.
Popular spells are spells who cost less to cast than your custom spells, someone figured out sweat spots who was cheaper or special ways to cast them.
Naturally this spells become more popular, the main reason to create lots of custom spells in earlier games was to rename them so they was easier to find.