That doesn’t mean the “they” here isn’t unclear. I wasn’t sure whose Mastodon handle Paul Graham shared. I certainly didn’t think OP meant he shared his own handle.
To be perfectly pedantic, this should only be confusing if referring to the Mastadon employees. Otherwise, if referring to the non-person entity, singular or plural appropriate syntax would be “it”.
They originated around the same time, but singular you was initially only used for addressing superiors/showing respect (using the plural second person pronoun as a singular for this purpose is still a thing in a bunch of languages), a few hundred years later “you” became the standard second person singular pronoun while “thou” fell out of favour.