Ramsey,
I agree with you that comparing these settings is tedious from the GUI. One thing I usually do to address this is to copy and paste each of the Compiler, Linker and XDC "summary of flags set" to a text editor (Notepad++, PsPad, etc.) and then compare them using a text-based editor. The nice thing is that you are even able to paste certain build options by using the Set Additional Flags button.
Hope this helps,
Rafael