I ran into an interesting issue: if you have a Viper unit that is not on the team and press any of the 'make weapons/armor/utility items available' buttons, the base item is stripped off your alien troops and cannot be re-equipped. Specifically, it states that the basic 'rifle' guns (including the magnetic and plasma rifles) are not equippable by the Viper.
The result is a trooper with no weapons or armor, and you cannot equip anything to them except utility items.

As a side note, none of the aliens can be customized in any way.