The second half of this warning is a clue to the answer for your and the original (from 7.5 years ago!) poster's question. The amount of material left by the roughing bit might cause finishing bit to break, etc.
If you are certain that your finishing tool can handle cutting the amount of material left after roughing you can safely ignore this warning. If not, change the "Machining Allowance" to be equal to or less than 20% of the bit diameter. e.g. roughing tool 0.375"; machining allowance 0.0075".
If I'm roughing out EPS foam with a 3/8" bit I might leave 1/8" or more for the finishing ball end bit to clean up. The foam is so "soft" that a 1/4" or even 1/8" ball end bit will have no problems shearing it off.