In Illegal Alien the Doctor establishes that the particular group he’s dealing with are time travellers from the 30th Century… so there’s an additional confusing issue regarding their appearance on the novel cover…
It seems likely within the fictional world of it all that the various types exist alongside each other at the same time in many cases, it’s just that on screen we didn’t see it… so maybe those Invasion Cyberman on the covers of The Moonbase/Cybermen novel were also lurking about on board the Cyber Craft, and likewise in the Tombs as well, just kept in reserve somewhere…
Remember that Mondasian Colony Ship in World and Enough Time? I've seen novels that survivors found themselves fighting against Neomorphs, meaning they were among the Cybermen in that ship. That ship probably has billions upon trillions of Cybermen of all the designs we've seen in the show's history, all in that ship, endlessly releasing more Cybermen. Like William Afton from FNAF, The Cybermen, They Always Come Back..
I also like to think that the surviving Cyberfaction, Mondasians and Neomorphs fought with the Cybusmen during Doomsday before learning the Cybusmen has a similar goal, leading to some becoming the ones seen in Closing Time
