yes "synthing at a loss" doesn't necessarily remove gil from the server by itself, however...
when i purchase that item at 1k and turn in for 300 GP that does remove gil from the system since i could also have NPC'd it for 300 gil... the item itself has an NPC gil value and i've destroyed that by trading it for an equivalent amount of GP (try this and you'll see NPC amount in gil is the same as GP value)
so in the case above, even considering the "synth at a loss" to not be a factor, i've still taken 3.2k gil out of the system
when i purchase that item at 1k and turn in for 300 GP that does remove gil from the system since i could also have NPC'd it for 300 gil... the item itself has an NPC gil value and i've destroyed that by trading it for an equivalent amount of GP (try this and you'll see NPC amount in gil is the same as GP value)
so in the case above, even considering the "synth at a loss" to not be a factor, i've still taken 3.2k gil out of the system