HOW they actually managed to ship their equipment (and I mean all the stuff they actually manufactured) from the factories to the front line beats me. I would THINK that they used larger crates for the gun exports, as that would have been a little more convenient than 1 box each. The only stuff I can remember to have seen concerning the shipment of goods is the Mauser factory boxes for K98k (that I think was pictured in "Backbone of the WH").
What I do know is that the Portuguese crates for the Metra M944 in no way resembles German WW2 made boxes! The hardware is non-German, the internal dividers in German boxes are normally made of oak, and certainly not pine which tends to break quite easily! The construction of the box itself is also un-German, actually rather "raw" compared to normal German box-making techniques. The "outside" cross bars underneath, the built in handles at the end etc. Not one little chicken stamp!? The rest of the stuff in the export deal all carries WaA markings. The norm is that German crates are WaA marked, but not so with these! There is a lot of details that doesn't add up, and none that actually does! (If you don't count the fact that the guns have been stored in these crates for a long periode of time before they were exported with them as solid proof of German manufacture!)
If they were indeed made in Germany in 1943 they must have been made after Portuguese specifications in "uncontrolled" factories, but I find that hard to believe.
I understand that people would like to BELIEVE the crates are German WW2, but there is just no evidence to support the belief! And as you quite right point out; there is no known GERMAN used crates for these guns documented either!
Personally, I have the gun from the box, but disposed the box years ago, as I found it of no interest!