If you have enough internal adjustment in your scope, you can zero at 100 with a 20 MOA base. And if you have a quality scope, it's no big deal cranking it down. I had an older Bushnell 4200, and the older models only have something like 26 MOA of adjustment, and that wasn't enough to zero at 100, it was zeroed at 300. Replaced the 20 MOA base with a 10 MOA, and I was GTG. Shooting a 6.5X47 instead of a 308, I didn't need a 20 MOA base, I found out.
But what you're talking about doing, using a 20 MOA base and a scope with a lot of internal adjustment (30 mm tube) to get a 100 yard zero, is done all the time by hundreds of long range shooters. Go to Zak Smith's web site, you can read all about it. In fact, he'll probably pop in here with a link soon.