I think I figured it.. the Galileo compiles with "-g" option which I guess produces debug information held within the object file.
Since I was asking the compiler to output to "stream_my_new_name.cpp.o" (instead of "stream.cpp.o" ) this was reflected in the output - but you can't tell because the output file is unreadable in a text editor.
I confirmed this by re-doing my test but in a different sequence..
1. Execute a build in Arduino
2. Find the object file you want - e.g. stream.cpp.o
3. Rename it so it won't be overwritten
4. Execute the the Arduino command line from a shell window using the exact command i.e. don't change any file names at this point
5. Compare the files, they should be same.
Thanks Coding Badly for giving me the hint about timestamps, that got me thinking about the debug info