I believe that the wind consideration in engine runups have to do with the engine stability, most notably fan issues at high power.
When you are standing still at high power the inlet is sucking air and any wind across the inlet is akin to angle of attack changes on the inlet itself. Some engines might not like this and even backfire/surge/stall (its hard to sell this product afterwards to a customer). While in other cases minute angle of attack changes could oucurr to the fan blades themselves setting up a flutter zone which might rapidly wear out the whole fan blade set.
Steady state winds are easily accomodated but gusting winds are not so easily defined in directionality. Its not a question of being boxed in and not getting enough air, it's the need to have smooth airflow at high power if you are anywhere near the fan blade flutter speeds.