"Subsequently, Scotty chooses to retire from Starfleet, become a civilian specialist, and promotes Geordi La Forge to captain, giving him command of the Challenger."
and
"After stealing away to the Challenger, Scotty holds the ship until the Tomalak's Fist travels back through the fold and destroys the Starfleet vessel to un-fold space and close the opening. But at the instant the ship implodes, Scotty is transported away -- unsure if he'll survive inside the toroidal continuum fold, but prepared for the possibility of death."
So technically, the Challenger shouldn't even exist anymore, going by the TNG Relaunch. Since Cryptic also ignored the ST: Destiny books... *shrug* seems to make sense they'd base the idea of Geordi captaining the Challenger on VOY: "Timeless" instead.