Lux passive is 1 source of damage, Lux auto is 1 source of damage, and Lux E is 1 source of damage. I don't know where you heard that, but they are most definitely 3 unique damage sources. Her passive isn't considered an auto attack, it's considered a spell. Thunderlords required 3 instances of damage, which is what you can achieve with Lux E auto combo. Regardless of how easy it was to proc, nobody ever complained it was broken. Riot never changed it, hotfixed it, or anything. They were fine with it, and so was everyone else. Nobody ever got on the forum and complained it was broken.
Also, electrocute basically wants 3 distinct attacks vs thunderlords just requiring 3 instances of damage no matter where it was from. Something like morg W or nasus E is one cast and applied something akin to a dot while in the pool, which counts as 1 attack, and is why it can't proc it (yes, I am aware it isn't a dot, but I believe it's coded in such a manner). You can still proc electrocute with 3 casts of a single spell if the CD is low enough and the time between them coincides with the internal timer of the keystone. You can even proc it off 3 auto attacks. There are still champs that can proc it like they've always been able to, most notably bard and lulu.
There's no reason it shouldn't still work for Lux. Regardless of its triviality to proc, it's abuse is combated by it's extremely long cooldown with no way to speed its CD along. Meanwhile comet has low CD, reasonable damage, and can have its CD reduced just by landing more spells. So why not use comet if its so good you may ask? I want to be well rounded. I don't enjoy having to go down the sorc tree just because I wanted SOME damage in my build. Here's my build. I get 2 runes that help give a little bit of damage, 2 runes that help me with vision control, and 2 runes to assist my ability to shield / heal others.
Instead I'm being forced to pick between a reliable proc with unreliable damage, or an apparently now unreliable proc for reliable damage if I want damage options in my build while still staying relevant to my team as a support. Basically if I want somewhat reliable (negligible)damage I either need to hit my whole combo, or spec into sorc tree, losing 3 rune spots to mediocre choices over team oriented choices which could actually be useful as a support player. Kind of kills the point of customizability if we're going to be forced into a certain runes.