The main reason why two single bores with regular cross-passages tend to be preferred for new tunnels is fire safety. If a train catches fire in a twin-track tunnel there's nowhere for passengers to go that is smoke-free, unless you build a separate evacuation tunnel. If you build an evacuation tunnel, then you might as well make it a bit bigger and put the second track in it, gaining all the benefits of simplified maintenance etc.
For shorter or lower-speed tunnels you can get around that using signalling restrictions or more powerful ventilation and/or more frequent ventilation shafts.
Long, high-speed tunnels require very careful design of the safety systems and operating procedures. The Gotthard Base Tunnel has two emergency stations (with platforms) and rescue trains permanently stationed and manned at both ends.
In the Lötschberg Base Tunnel there are strict rules about the order in which freight and passenger trains can be flighted to prevent a passenger train being trapped between two freight trains, and the evacuation plan if a train were to stop in the single-track section literally involves commandeering all the public PostAuto buses serving the towns in the Lötschberg pass and sending them through the uncompleted tunnel bore (which serves as an evacuation tunnel) to pick up the passengers.
I'm assuming the Chiltern tunnels have so many ventilation shafts over such a short distance to cope with 18tphpd without as many operating restrictions. Twin bores will be a key part of that.