In fact, snapcraft’s cleanbuild is practically creating a new LXD container and run the build in it. The point is to provide a clean environment while not contaminating your working environment and is VERY useful. The LXD installation is from snap or debian package shouldn’t really matter much(though personally I never tried the snap installation), if it does then maybe there’s a bug to deal with.
Here’s a tutorial I wrote for making an LXD container for snap developing without the cleanbuild’s “feature” that destroys the container everytime a build is ended: