Hi.
First, I think there is a misunderstanding : the message box displays information about both files such as date and size to help you identify wich file you keep.
You also have the options to rename "old" or "new" file if you want to keep both. : Strike this, misunderstanding seems to be on my side 
Then, you could also :
- Use the find duplicates function and decide on which settings the comparison is made (checksum being one of them)
- Directly force MD5 calculation to check in flat view if you have dupes
Here is a little button that will add a "Checksum MD5" column and compute MD5 on selected files
Calculate MD5.dcf (312 Bytes)
This works best when you have only a few files, otherwise, searching for dupes is imo the superior option. It is in first few commands in the "Tools" standard menu.
Note that MD5 calculation speed may vary depending on file size, number of files, drive type (hdd/ssd) and cpu.