It does not seem to me to be any real source of confusion. Certainly not one that could have safety implications. Simply a matter of context.
- 1013.25mb is the pressure at mean sea level of a standard atmosphere.
- QNE (of an airfield) is the altitude of the airfield relative to the standard atmosphere.
- Flight Level is any altitude quoted relative to the standard atmosphere.
- An altimeter must be set for QNE (i.e. set to 1013) in order to fly a Flight Level or fly an airfield pattern when required to fly relative to that airfield's QNE.
It seems improbable that an aircraft requesting an airfield QNE could possibly be considered to be requesting a pressure setting (which never changes) so I do not see how confusion could arise.
Although if the answer came back as 1013 it may give the commander pause for thought ;-)