I did mean 25% faster, though it was a guesstimate. That was comparing Agilex to Agilex D, not Cyclone V to Agilex D.
FPGA logic in simple terms consists of LUTs (look up tables, used to implement gates) and registers. The LUTs can be chained several times until they connect to a register. Registers are clocked at a frequency.
Now the max frequency is calculated using the maximum time from a register output, through a bunch of LUTs to reach another register. So it depends how long the chain is.
Its more complex than that in reality since there is also the time for the clock to propagate and to route the signals around. Fortunately the software takes care of that.
I don't really know how maximum frequency is specified in the specs, but I guess it'd be something like an ideal register->single LUT->register without much routing.
If you really meant 25% you probably were not reffering to the clock speed/MHz, what were referring to?