Both are right.
The thing about riding bikes is that real value only seems to come after, say, 2 or 3 hours riding. Hopefully no-one other than a snow-bound pro (I spoke to a GB dev squad rider recently who had to do a minimum of 20 hours a week on the turbo during the recent snow) is sane enough to spend north of two hours on the turbo….
Anyway, for a long base session, I would do 10 mins warm-up and then 90 minutes in zones 3-4, followed by 10 mins warm down.
For intervals, I never do more than an hour, but I am completely battered when I climb off, and often find walkiing up the cellar stairs tough.
If you're trying to build fitness, then steady sessions where you are working at up to threshold (without a heart rate monitor, this is approx the point when your breathing becomes laboured and your legs start to burn) will be better than short, interval, sessions where all you do is develop a sort of "explosive" strength without the underlying fitness.
However, ignore all the "fat burning zone" nonsense.
I know what you mean about a bad chest and the cold weather. One thing to consider for riding outside is, rather than MTBing which is often stop/start (opening gatres, etc.) steady road riding might be beneficial without the downside of illness. Try not to go so hard that you're breathing in great lungfulls of cold air. Oh, and ride wearing a buff over your mouth.