About the Apoc-style equipping:
In my recent experience I found that managing soldier inventory via the Base Soldier inventory to be buggy: Sometimes the changes do not save, sometimes they revert to what the soldiers had months ago, sometimes not recognizing that I have items on the "ground" in the first place unless I have them in excess.
Equipping soldiers via the Craft Inventory (in geoscape, not during battle start), on the other hand, so far has been bug-free for me and working as intended.
Not sure what is so different between the Inventory in Soldier Screen and the Inventory in the Craft Screen that leads to such different results.