Okay, so when valving a shock you use a stack of one #. So all #30, #40, #90....
I've heard of "flutter stacking" which involves putting a small shim over the the large bottom shim. This is to soften the shock over light bumps but it keeps the rest of the valving for harder bumps. I read it as a way to get progressive valving out of coil overs before bypass shocks. Pretty cool 
Yes a flutter stack does just that. But as to how thick the shims are and how many you put in is part of the tuning process. Both on the flutter and the rest of the stack.
Most of the time, when using a bypass shock, the coilover becomes a coil carrier. i.e. the guts are ripped out and the shock just holds the coils while the bypass does the work. You are correct that flutter stacks were used more before bypasses existed.
Think of shocks like this, the harder you push them the harder they fight back. They are Dynamic pieces of equipment. Springs compress at a certain rate no matter how fast or slow you go, they compress in a predicatable manner. They are Linear.
Stiff springs need softer compression valving in the shock to ride smoothly. However because stiff springs typically do the work of the suspension they are bad at soaking up larger bumps at high speed because they dont fight back the harder you hit them.
Softer springs need stiffer compression valving to maintain vehicle control otherwise you end up driving a sloppy slinky P.O.S. Because shocks are dynamic and can soak up larger bumps with easy, the stiffer the compression is the faster you can go. But you have to match that stiff compression with a soft spring or you're back to riding a brick.
Coilovers were designed from conception to run springs soft enough to net you 50% or more of compression of the spring at ride height. I like about 60% for crawlers.
