I took this down from the web:
"QNE:
When the ISA mean sea level standard pressure of 1013.2 hPa is set on an aircraft altimeter subscale, the height so indicated upon landing at an airfield is known as the QNE reading. More widely, this is also the PRESSURE ALTITUDE, which is alternatively defined as the height of any level in the international standard atmosphere (ISA-see above), above the level corresponding to a pressure of 1013.2 hPa"
The question you raise is whether the QNE is the reading on the altimeter with standard pressure set, or if QNE is the actual pressure set. In the quotation above you can see that what you are talking about is "QNE reading"
This quotation is from an ATSB Accident report:"QNE is the standard pressure altimeter setting of 1013.2 hPa that is set for flight above the transition altitude."
All of the above; QNH, QFF, QFE and QNE are pressure settings and the abbreviation's can be found here :
http://www.aecma.org/Publications/glossary/gq.htm
But enough about that. The question here was the definition of TL and TA and how they prevent conflict. I hope those questions have been answered.