A War Convocation is a special type of Formation, made up of a Cult Mechanicus Battle Congregation (which is itself a Detachment), a Skitarii Battle Maniple (which is itself also a Formation) and an Imperial Knights Oathsworn Detachment (which is... a Detachment).
The Skitarii Battle Maniple is not chosen with any reference to Battlefield Role such as HQ or Troops; instead, like most (all?) Formations, it simply tells you which units you must take in it.
In terms of choosing your army, Battlefield Role is only of importance for Detachments which use a Force Organisation Chart.
The Cult Mechanicus Battle Congregation, which forms part of the Adeptus Mechanicus War Convocation, is one such Detachment, which has a minimum requirement of one HQ and two Troops choices. It also allows you an optional Fortification slot, so you would be able to take a Void Shield Generator or a Haemotrope Reactor as part of it.
It's also worth noting, as you mentioned Drop Pods, that units cannot begin the game embarked upon an allied Battle Brother's Transport vehicle. This makes taking Drop Pods with the intention of giving your Skitarii/Cult Mechanicus units a ride not possible, as per the new rulebook FAQ.
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