Now I've always played it so that if you use a doctrine that costs a certain amount of points per unit, the cost is applied to each squad. For example, if you have a Command Platoon consisting of a Command Squad, a Fire Support Squad, and a Special Weapons Support Squad, and then purchase the Carapace Armour doctrine, you'll end up paying 60 points (20 points for each squad, in other words). I've never seen this applied any other way.
However...
The wording in the Infantry Platoon section (p44) supports this:
"Each Platoon counts as a single Troops choice on the Force Organisation chart when deploying, and is rolled for collectively when rolling for reserves. Otherwise they function as independent units."
See? Nothing there to contradict the way every IG player buys doctrines for squads. The required Command Squad and 2 to 5 Infantry Squads are all units (the text above states as much) and all operate independently as separate units.
But the text in the Command Platoon section (p38) is considerably different:
"A Command Platoon counts as a single unit for army selection, deployment and reserves purposes. However, each sub-unit may deploy or arrive in a different location and act independently." (Emphasis mine.)
Note that is says the whole Command Platoon is a single unit for army selection, the process of which includes choosing doctrines. So does that mean that if, to continue using the example, you take the Carapace Armour doctrine then you'd only pay 20 points no matter how many Support Squads you took?
Note also the reference to 'sub-units'. This implies that Support Squads are 'sub-units' and not 'units' (in addition to the whole being greater than the sum of its parts here).
The only argument I can see against this is the fact that most doctrines refer to 'Guard Infantry units' and the description of said units (p55) refers to all the Support Squads separately. This is, however, somewhat countered by the use of the words: 'along with'.
So, any thoughts? Or am I missing something really obvious?