How to calculate the effective junction temperature of the FPGA?
Is this junction temperature is expected or some mistake in the
consideration.

It's not a mistake unless you want to run the device without considering the junction to case thermal resistance. \$\theta_{JC}\$ is the main route for heat to travel (to a heatsink/fan) whereas \$\theta_{JA}\$ is a parallel route that is not anything like as good for removing heat.

Any insight would be greatly appreciated

Noted!