check the FAQ on the GW site as IIRC, the banner *must* be on the table in order for units to benifit from it... (otherwise, if it's still beautifully ambiguous, then yes you could technically use it even if it is hiding in a chimera, as awkward and silly as it seems!)
i think you'll find that running carapaced vets is far superior to storm troopers in every way... against MEQ's, that possible 4th plasma weapon can equal total annihalation to smaller assaulty type squads like vets, termies, chosen and similar. (ie: 3 plasma guns + plasma pistol).
plus, the power fist alone is worth the swap. most marine players won't hesitate to throw their marines into your guard at the very first oppertunity. they'll start to cry once your sergeant kills a possible 4 marines/turn on 2's! and again, the vets can throw out a deceptive number of attacks as they can take that pistol + CCW combo - even T3 hoards like gaunts will falter to that.
the rules for the optional chimera turrets are in Imperial Armour vol.1
they include the autocannon, twin-linked heavy bolter & IIRC, multi-melta! (quite appropriate for a commissar's ride!
)
cheers!