MetaChem doesn't alter the profile, it's explicitly described as a MOD: Immediately after placing each of your troopers with MetaChemistry on the table for deployment, you may roll on the MetaChemistry Table once to determine that trooper's extra MOD or Special Skill. So the only question really as @RobertShepherd pointed out is why you get the MODs from Cover when using a 'Mate - but given that it's explicitly in the examples I see it as an exception to the general Attribute value/MOD rule.
You need to learn the difference between explicit and implicit. It's certainly implied that arm is a mod because nothing else is specified. But let's not oversell how clear it is.
"to determine that trooper's extra MOD or Special Skill." to me, it is also implied that it is not a MOD but a special skills, named Natural Armor, which has an automatic effect of +1 ARM. MetaChem gives Natural Armor.
