How is `cp -R` different from CTRL-C/CTRL-V?
When copying and pasting via Finder there is certain meta-data that is maintained that when using cp -R it's not.

An example is when copying and pasting via Finder the created/modified date/time stamp of individual files are maintained to that of the existing meta-date vs. using cp -R where both the created/modified date/time stamp are set to the date/time of the copy operation.

On directories when copying and pasting via Finder the created date/time stamp is maintained to that of its current value and the modified date/time stamp is set to the date/time of the copy operation. vs. using cp -R where both the created/modified date/time stamp are set to the date/time of the copy operation.

Now if you use cp -aR the created date/time stamp is set to the date/time of the copy operation and the modified date/time stamp is maintained to it value it had at the time of the copy operation.

In essence copying and pasting via Finder maintains all meta-data attributes that are supported by the destination filesystem and to get the most possible meta-data attributes maintained using cp then additional options must be used.  Have a look at the cp man page for additional command line options.

FAT32 does not support all of the file attributes that HFS+ does, however copying via Finder preserves more then cp regardless of the options implemented.