My advice to anyone who needs to anneal Aluminium as part of a more complicated process is to complete as many of the machining processes as possible while the material is still hard. You’ve brought a hard machining grade so therefore use its' properties. Annealed soft Aluminium is difficult to machine and by this I mean; drill, mill, turn, cut etc.
You are completely right, but the order of the process can not be changed. The Al-alloy won't get machined after the furnace process, so this is not as important as the discolouration.
Yes, his statement was confusing me too... Maybe he meant that the thickness of the brownish layer is too low and therefore the electrons would penetrate deeper sections (leave the brownish layer on its backside).
As you know, Al forms a layer of Al2O3 on its surface, thus the color of the Al-piece will absolutely affected by this layer. In the case of your alloy, Mg and Mn are present. These elements, in the presence of Al2O3, can form spinels (MgAl2O4 and MnAl2O4). These spinels can be transparent, white, and colored. Both of them can be brownish. That is why perform XRD is very important to know if they stand behind the color of your sample.
The best way to do SEM is to take a cross section. This way you will be able to see the outer layer and the sample bulk, and then analyze the outer layer. You can do line scan starting from the sample edge moving towards the bulk to see elements concentration gradient. However, XRD would be the best way to do the analysis.