The Core starship, as far as I recall, does turn up in normal games- although in my opinion it could do with a new bag of tricks so that it's not just a Mk5 flagship by another name...
As for the Imperial Spire Super Dreadnought, there should have been two in with the very first fleet to come through the transceiver- although given the number of other ships coming through at the same time, it might be easy to miss. Those are the only two, as far as I know.