Unfortunately the only comparison tool addresses the Runtime (.mer) application on a terminal and the one within the development PC...It is a binary checksum returning only Identical or Different...The individual differences are not listed....
The tool is available within the ME Transfer Utility applet.
You can compare the components inside the .apa by restoring it and exporting the components, such as the displays. The displays are exported to XML and you can compare the XML text using Notepad++. That will show you the exact differences. The same can be done for parameter files and message libraries but excel would be easier for those. Check out this video https://youtu.be/eJsO5PRPHoQ