There are just some things that the Fixture Builder does not accomplish. I find that manual editing in an IDE or text editor will clean up the untidy bits...or a dedicated .XML editor will work as well.
I do notice a difference in the amount of data the fixture Builder saves files from the files that are saved from within the console/desk itself...your mileage may vary.
I prefer an IDE for editing; you can collapse and expand the dataBlocks instead of trying to read a wall of text, ;). The console is best but the GUI system of a single window and paging through things is tedious. Having all the sections exposed, as in the fixtureBuilder, is not tedious-but lacking in some ways as I mentioned.
Rex