jazzbo is right about this. Shntool compresses flac at default level 5, regardless of what compression level the original flacs had. Shntool always applies the default settings of whatever output format you are using.

Secondly, in order for shntool to do it's job, it always decompresses the files to wave format, does what it has to do, then compresses the results to whatever output format you specify. It does not merely shift bytes from the front of one file to the next. That would not work, since it is, as jazzbo states, the audio stream that shntool works with, not all the data in the file. In fact, if, for some reason, you had a set made up of a mix of shn, flac and wave files, shntool could easily work with all of them at once. This is because it converts everything to wave format.