Hi,
The differences between 10CL016 and a 10CL025 is the number of logic element. Higher the no. of logic element, the more the logic in the design that it can be loaded in the FPGA. It should be better to compile the design in 016.
I would say the file format are not the same between both of them. But both of them are meant for PS configuration.
You may refer to link below for more information.
https://www.intel.com/content/www/us/en/programmable/quartushelp/13.0/mergedProjects/reference/glossary/def_rbf.htm
https://www.intel.com/content/www/us/en/programmable/quartushelp/13.0/mergedProjects/reference/glossary/def_hexout.htm
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