We've had a micro on a shelf for 10 years and never even knew that was a guideline until you just posted this. We have about 1 inch all around... I think you'll be fine.

Each brand/model likely has their own specs. We gave ours just barely under the full specs, which was 3" on each side and not as much at the top. We have a 2 cu ft microwave that's pretty powerful and I didn't want it overheating or give it a reason to quit. It also depends on how surrounded it is. In our last house the shelf was mostly open on one side, so I wasn't as worried about space on the other side.