Well I sopose you can look at it this way.
#1. Whats the point in spreading out advanced fusions, just means more of your base destroyed, if the enemy can swoop in and blow up 1 in a single strike, game is over anyway, so might as well make it quick and put them all together to keep the damage at a single point.
That way only your base area is destoyed and the damage is localised, instead of spread out over a huge area.
Build Regular Fusions instead, and keep them spread out, more targets means you buy more time to react to an attack.
Ok, so whooptie doo, you still got another one left that didn't get blown up.
I can guarantee you that losing the first one took out some pretty important stuff that will take a long time to rebuild.
If you're speaking about a Heavy Bomber attack(which it almost always is) using Hurricane/Pheonix, that super expensive Nuke that you call a Advanced Fusion is going to die if as little as 6-7 bombers hit their mark in 1 strike.
#2. With Moho Metal Makers (MMM), there is no excuse for not spreading them out, their death explosion is minute in comparison to other high cost resource buildings.
Keeping them spread out won't damage your entire base as result.
Honestly, if you're worried about sombody striking at your advanced fusion, you've been porcing too long and deserve to die.
