Again the GE Empire having faster FTL is being a drastically overrated advantage, the GE isn't a von Neumann AI swarm they still need to find the planets and when they attack have sufficient fleets to take over the planet.
Average Empire fleets are just a handful of ISD's which I remind you in both canons cap at 25k, will also have to remember that the GE can't commit all of those ships because they'll have to defend their territory, assuming they use 50% of their ISD fleet because literally only ISD's have the fire power to beat a strike cruiser you're looking at 80 planets per Star Destroyer to conquer.
The ISD's Navy isn't big enough to blitz the Imperium's defenses and realistically they'd only be able to commit 12k ISD most of which would die before they realize anything below an ISD will be literal fodder when invading Imperium territory.