We have an argument regarding the " Minchat Nissachim " , if not brought together with the Korban. Which should be brought first , the Mincha or the wine Nissachim. The Gemurah does not Poskin Halacha which one is right. Now you should say there is no reason for the Gemurah to Poskin since it is not a " Halacha LeMaiseh " issue ( as Tos . 45 B " Halacha " ). My question is as follows : there seems to be a very similar circumstance in which the order of wine and bread ( Mincha ) are important. Shabbos . The order of Kidduish and Hamotzeh. We know, that normally , bread precedes the Bracha for wine. But on Shabbos we say on wine first ( and that is one of the reasons we cover the Challah ). Can there be any relationship between wine / challah and the Mincha / Nissachim ? And if so, our Gemurah does have a Halacha impact.
It doesn't seem to me that there is a relationship, as the Gemara here seems to hinge on how to understand the fact that whenever the Pasuk discusses these two items, it always states "u'Minchasam v'Niskeihem" (i.e. Vayikra 23:18). The order of what comes first in Berachos is similarly determined by the famous Pasuk "Eretz Chitah u'Seorah Gefen..." (Devarim 8:8), where Chitah (wheat) comes before Gefen (wine). As you noted, one of the reasons given for covering the Challos is due to the fact that a Berachah is normally recited on bread before wine, according to all opinions, based on the Pasuk above. Being that the Gemara in Berachos (41a) which mentions this Halachah doesn't mention any other opinion based on our Gemara in Menachos, I don't think the two are related.
All the best,
Yaakov Montrose