I'd venture to suggest that anything up to, say, 10 minutes as an occasional planned dwell time on a longer journey is probably not at all undesirable but rather helpful, building resilience in to allow for a number of things that can cause a train to lose a handful of minutes. I've noticed it to be quite a common occurrence in parts of Europe, even in countries with relatively short "long" journeys like the Netherlands and Belgium. Oftentimes the dwell is shorter (3-5 minutes) but more frequent.
Certainly here it seems tough to fulfil a station stop with bicycles, wheelchairs and luggage-wielding reservation-holders, plus dispatch with the endless hustle alarms, in the apparently standard 1-2 minutes