Is the answer contained within your first posting?
Why does the alert logic consider the aircraft "in the air" when the MLG are on the ground?
For the purposes of TRU warnings, that's wrong. Are there other systems or circumstances under which MLG on the ground but nosewheel in the air should be counted as "in the air?"
Seems the problem would go away if the TRU alert logic looked for "MLG not on the ground" instead of "aircraft in the air" as a gating condition.