The timetable is there to make the railway work not vice versa - in your own favourite phrase, there is no need for the tail to wag the dog!. There are places where it needs to be accurately followed, and places where there is benefit in a bit more flexibility. Following it 100% of the time just because you think it looks professional is wasteful and pointless. Just like in Clapham junction, there is no reason that London bound trains need to follow the timetable at all in OOC - arrive when they get there, probably normally a minute or two ahead of the timetable, and then depart as soon as the last passenger disembarks and the (electronic) signal is green. If the train arrives early in Euston, great, it gives a few more minutes recovery time for the next service, and means that a thousand people arrive pleasantly impressed and with an extra minute of life, rather than sitting frustrated at the platform in OOC wondering why the train is delayed.A brand-new, multi-billion-pound high speed railway should be aiming for 100% right time and able to have many days of the year - more than not - on which that is achieved. Ask the Japanese. This is not like eking out the last bit of capacity between 1630 and 1830 out of Euston on LNR. This is about designing something to work properly. A railway working properly is one operating precisely to the timetable.
But there will always be the ones that don't, far more so than a commuter railway. There'll be the person needing the ramp. There'll be the one needing help with their bags. There'll be the one that can't read the PIS, either because they're confused or because they have a sight disability. Etc.
The dwell times have precisely nothing to do with how intertwined or not they are with the conventional railway. They simply reflect that it is not feasible to board 500 people onto a train reliably, every time, within 2 minutes.
Northbound, they can't depart early, but if the train is a minute late leaving because this departure had more than its usual share of slow passengers, there is time to catch that up before reaching Birmingham, and much better have 10% of trains very slightly late but with padding to catch up than every train wasting time.