For the same reason it wasn't possible at the time for a third-party to make N64 cartridges themselves to avoid Nintendo's fees. But I assume these lockout chips are replicated or circumvented by now.
Nintendo's boot code is under copyright and thus cannot be used. So the boot code distributed with Libdragon is signed by finding a hash collision with a brute force tool running on the GPU[1]. Fun stuff!
[1] https://github.com/DragonMinded/libdragon/tree/trunk/boot#bu...
And on top of that, libdragon's IPL3 doesn't just blindly copy the first megabyte of ROM code into RDRAM like the official Nintendo one does, but actually expects the ROM data after it to be a full-blown ELF executable, which it parses out and copies pieces of to the specified places.
Pretty slick stuff.
But it's legal to use the Sony and Nintendo trademarks in a similar way. The court ruled that since they are checked by the console, there was no way not to use them, and Nintendo lost their protection by doing so.