I am working on a remodel job and we are having trouble getting a blotch free clear coat. We are using water based polyurethane on new cedar, no stain.
Blotching comes from the wood soaking up the clear coat unevenly. That can not only be an issue with staining wood, but also natural finish in some cases, possibly due to the presence of oils. One way to minimize it would be to seal off the wood with a dewaxed shellac first. Good news, it dries fast and you can put down your polyurethane after 1 hour.