Do 2-hexyne and hexa-2-yne mean exactly the same thing?
For 2-hexyne, the extra naming possibility isn't really a help.

However, consider a more complex molecule, say, a hexynol.  It has both an alkyne and an alcohol.  A name like 2,4-hexynol would be very confusing.  Which group is at carbon 2 and which is at carbon 4?  That is why IUPAC doesn't provide for that possibility.  Instead, Writing it as hex-4-yn-2-ol is actually clearer and more understandable.