Why are there some difference bytes between the base and revision periphery image even after performing the revision design flow in CvP?

The differences could be due to the JTAG USERCODE value in the option register. When the Auto usercode option is enabled, during each compilation the checksum values are update automatically into the JTAG USERCODE registers in the programming file which are different.

In the Device and Pin options under General tab, turn off the Auto usercode check box. This enables the JTAG usercode option set to default value 0xFFFFFF. You can set  any hex value for the JTAG usercode as long the values are the same for base and revision mode before each compilation. Make sure the other options settings in Quartus® II are the same for base and revision mode before each compilation.