How does the government know which token a ID card generated? The ID card itself generates (for each service a different one) and encrypts it. Not even the card reader can read it. It is a encrypted channel between the card and the ID-server for the site/service. The pseudonym function does not identify a person but a card.
The government doesn't know which card a token from a "pseudonym function" belongs to. The government can identify a person when the ID function was used, of course.
Again, it is a random token the card generates internally for each service. It is non transferable! If you get a new ID card, you can't use it login to whatever you used your old card for. (You would need something else... say an email :-) to tie the knot back to the old identity or whatever.) Which makes this function, the pseudonym function, very bad for random accounts (Edit: meaning longer lasting online identities like forums or whatever). I guess eaglemfo didn't knew.
It's more for like "yes, yes, I'm an adult, now give me this pr0n movie which I pay for with my anonym prepaid card" kind of deals.