If FSM B has registered output logic then as long as the FSMs are identical (i.e. the outputs have identical timing and responses to inputs) the two FSMs should have synthesis results that should be identical. If they aren't the same then you are likely looking at some sort of boolean reduction algorithm issue with the synthesis tool. If they aren't registered and you have identical output timing then you will have two entirely different implementations with the FSM B having much worse Fmax due to the combinational paths.
Might be interesting to make a suite of FSM descriptions (small, medium, and large) to test this out and see if there are any differences between the various synthesis tools (e.g. Synplify, Leonardo, XST, Quartus-II, Vivado) might be very useful to know what is the optimal method of describing an FSM for each tool depending on the complexity of the FSM.
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Come to think of it, this might be an excellent school project. Determine the results of the following matrix: HDL language, FSM complexity, Synthesis tool. That's like 30 combinations