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In the UK at least, we usually calculate the flight level which will give at least 1000ft above the highest altitude.
In the London TMA, where the maximum SID altitude is 6000ft, the lowest FL will be that which equates to an altitude of 7000ft or more. So in times of low pressure, the lowest FL might be FL80. Conversely, in times of very high pressure we never use less than FL70. So it can take a long time to get from 6000ft altitude to FL70 or above, and this can prove embarrassing if you're not ready for it.
(For example: QNH 1040. 6000ft Altitude is approx FL 52. To climb and get separation of 1000ft above traffic at FL 70 you need to climb 2800ft instead of 2000ft. It can cause some tightening of the sphincter if you're trying to jump the stack!!
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So to answer your question more succinctly, the controller should know which flight levels are separated from altitudes and which are not.