A 2 car 168 (or 165) is almost always* sufficient for the level of traffic to Stratford, so a 5 carriage train would be overkill.
The service at present isn't brilliant. Stratford-Upon-Avon to Leamington Spa takes about the same amount of time by train as by the X18 bus, which is every 30 mins (train is every 2 hours...) and can drop you in a more convenient location.
If you want to go to London from Stratford and can drive, it's a lot quicker to drive 15 minutes to Warwick Parkway and catch the train from there, especially if you don't live near Stratford station.
Stratford-Upon-Avon - London via Warwick Parkway would be a good contender for a bus+rail combined ticket.
In addition Chiltern never had any replacements for the 172s, which stretched the 165s a bit further.
Indeed, though the 172s lacking tripcocks meant they had pretty limited use at Chiltern.
If you gave the Leamington Spa - Stratford-Upon-Avon/Birmingham to WMR, that would compensate for the couple of 172s Chiltern had out.
You are totally right that the flexibility is reduced, and seat number wise offer a marginal gain over a 4 car 168
I'm concerned about Wembley match days. Currently, Chiltern shuffles maintenance about to get long 6-car formations on match day shuttles; the current 4-car 168 equivalent capacity of the Mk5As is going to be insufficient for match days.