I feel like a major wuss for admitting this.

The DLC is played for humor the entire way through but the whole thing actually crossed a line somewhere because there's some stuff that genuinely had me squirming in discomfort. Maybe it was because the body horror elements were so prominent the entire time.

When I accidentally created the horrific abomination of a Robo-Brain from a Lobotomite, the thing laughing about it's new life, I got REALLY uncomfortable.

I was even freaked out by the midget Death Claw.

I think it was a bit like being in a cartoon, everything should be funny but when you're playing a character as serious as the courier, it's a bit like being dumped in a Nightmare.

Am I alone in this?

I think you're overthinking it.
It's not really that dark.

It's typical fallout. Silly or retro futuristic facade, scary event and story.
It's dark, sick, humour in a dark, sick world were they put isotopes in cola and do all kinds scary things.

It did'nt cross any lines that are unacceptable.
The scientists were clearly never virtuous angels.
Only Mobeus was good or neutrel.
Seeing how things were made in fallouts scary, dark world, was never going to be pretty.
You say secret science facility, you expect some dark and scary stuff.
It's more 50s scifi movie style facade. Always fun.

Under the humour it's sad, and scary.
But no more than any other fallout thing.

The story behind other things is scarier.
The vaults, blowing up the world to make it anew, that's far worse.
The accounts of after the great war, that's truely scary.