This is the default setup you will run into on any ppc64-linux host. It's definitely annoying that you have to workaround this in weird ways.
I don't follow. Why would you ever want to build the stage1 compiler as a cross-compiler and then do a "bootstrap"? I don't consider starting the process with a native compiler as a "workaround", but as proper practice. Otherwise, as I said, you have the wierd situation where the stage1 compiler is a cross-compiler but the stage2 and stage3 compilers are native, which gets seriously in the way of debugging a bootstrap problem.