Jean Elcard
The Flavournator
Flavor Start does drastically increase the time it takes to set things up. I've never had it take as long as you mention, though - but there is a hefty increase.
You are right. The culprit is the relatively new Isolation preference for the Sidar and the Grigori (just tested it). While the max path calculation currently necessary for it to work is bearable on small maps, it eats away more than half a minute on huge maps. If I cut this calculation you won't recognize a big difference between the loading times with or without FlavourStart. I'll try to think of something faster.