I find that the difference between road and trainer is huge. The resistance is very different and so much more constant on a trainer. However nothing beats a quality session on the trainer in winter time when temperatures are too low for any efficient, high intensity outdoor training to take place.
When I do train indoors it's (almost) always with wattage to maintain a certain level of control over what I am doing.
That said temperatures have to be at least below -5°C for me to pick indoor training for intervals.
During x-mas I had my planned "off season" and did mostly easy sessions on the trainer to maintain cycling specific fitness and prepare for 16 days on Gran Canaria, and it worked out great. My shape was much better than the year before when I'd used my MTB to ride trails in the same prior period. The use of an indoor trainer definitely didn't hurt, but a generally improved fitness over 2011 was also to blame.
As for Obree... he definitely knew his body well, but if his methods can be recommended for other people I'm not too sure. They seem rather radical and very mentally demanding, something not suitable for most and definitely not me. His book was an enjoyable read though, but for example "Cutting edge cycling" by Hunter Allen and Cheung has been far more informative and useful for me.
Addition: Why I don't really like indoor training - I produce a helluva lot of heat and sweat. Two sessions (1 hr at threshold each) and my Zero pedals were rusted, bleeding.. my shoes were dripping and had to be dried..