Dwell times are not significantly longer. The passengers, unless stupidity is a contagious disease transmitted by season tickets, will learn how to use them properly as they have done in other places with double-deck commuter trains like Sydney, Paris, Germany, commuter lines near New York City and southern California to name a few.
To get a 40% increase in space is well worth it, and not future-proofing the new tunnels is criminal.
Please note that I said "for all their additional cost and incovenience...". I agree that on networks where the infrastructure has a loading gauge that universally can accommodate double deck stock, the decision may be a little easier. The fact is that in the UK, the whole route, i.e. from Reading to Shenfield, Abbey Wood, and now maybe including the WCML to Tring would need to be rebuilt to at least GB+. In addition, the standard platform height in the UK is 900mm which means either that double deck stock would need three floor levels with very limited accessible space between end doors over the bogies or the trains would need their own platforms where they shared running with the national system. All this would make project much more costly, - probably leading to its abandonment. And all for a modest increase in capacity per train.
As far as dwells are concerned, both Thameslink and Crossrail should be capable of frequencies as much as 30 tph. At that level, there is an optimum ratio of train capacity vs access routes (doors) that gives the necessary performance. If trains capacity was increased by having both upper and lower saloons, the door capacity would need to be increased accordingly.
The highest rates of passenger loading and decanting is probably achieved on the Indian commuter networks. Here trains are wide very long and single deck, (not accounting for those travelling on the roof). I've travelled in double deck trains in NYC, The Netherlands, Italy and Paris. In every case, the ingress and egress of passengers is far slower than any of the high density services operated by single level stock.
Crossrail is effectively an extended metro service, just like the London Underground Metropolitan line into Buckinghamshire. Like the Met and Thameslink, Crossrail's trains will have wide open vestibules between coaches to allow rapid distribution along the train. Linear distribution along the train is impossible on multi-level stock as it would involve the use of stairs, either up or down to each of the main seating areas, - on a moving train, all slowing the movement of passengers to a crawl.
Clearly capacity per train length can be increased by double decks, its benefit is very dependent on the number of stops and service frequency. We mustn't confuse individual train capacity with route capacity.