There is something very confusing about the file organization under OSX.
Yes. The finder hides certain directories from searching. The binaries don't show up because they're hidden inside of an "application" (You know that "foo.app" is a directory, right? In finder, you can use right-click and use "show Package Contents", and THEN you can search.) Build directories are hidden because they are system temporary directories (party Java's fault.)
You should only have to find "/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin" once, in order to put it in your path (unlike the build directories, it doesn't move around.)
But you don't need to search for them, because the message window will SHOW you the directory names if you turn on verbose compilation.