"Are any of these things actually necessary?" No. If it's absolutely necessary, the firearm is defective. But a lot of them are very worthwhile improvements.
"Do the benefits they claim to offer justify the cost in cases in which they actually function perfectly?" Depends. I've installed a couple of extended thumb safeties on 1911s. They were not drop in, but they function perfectly and I'm very, very satisfied with the addition.
I will say I see what you're talking about regarding modifications though. There's a lot of "I"m installing this because the stock part might not be flawless at 25,000 rounds. Lots of people wondered about the polymer mainspring housing on my Colt 1991 when they were first introduced. Mine has been flawless. And I'm sure there were folks that decided to change it, did it themselves, and bent a spring or dinged the metal around the retaining pin.
So I guess the fundamental answer to your question is "sometimes it's worthwhile, sometimes it's not." Remember, you heard it here first.