Could you add a string setting in which you can manually list the prototypes that do not need to add pipes?

I'm unsure of what you are trying to achieve with this?

Mods can already include their own entities to a blacklist, each type of entity can be toggled in settings.

Are you hoping for a custom string, where you can just add your own exclusions regardless of settings?

Yes

Any particular reason you would need this indead of adding items to the existing blacklists?

Each type of entity?
There's 3 toggles: Assemblers, Refineries and Chemlabs.
I don't see a toggle to exclude pretty much everything in Space Exploration.

It's not that it's not working, but it's breaking pretty much all of the graphics because the pipes aren't anymore at the positions of their respective 'models', and that's irritating the hell out of me.

So where's this blacklist at?

Everything in Space Exploration will be some variant of Assembler, Refinery or Chemical Plant.

If you want to build a blacklist, see the faq.
https://mods.factorio.com/mod/assembler-pipe-passthrough/faq