Good question. Typically when I prescribe these workouts (MSS) I use a timed recovery only because if they are using a power meter and no heart rate then they have something to adhere to. However, with this specific workout type I'll usually set the recovery time at 2-3 mins since most anyone would be back into zone 1/2 by that time period. Certainly, using the HR method works just as well and as you get fitter you'll find that time period diminishing.
Exact recovery periods for this phase aren't usually too critical though - The real adaptation comes from adjusting recovery times during vo2 and anaerobic work later on. Doing a 3 min vo2 interval with a 3 min recovery is a MUCH different workout than a 3 min/1 min recovery.
Hope that helps and good luck with your season.
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Current Bike Collection:
2008 Redline Monocog Monstercross
2003 Alan Carbon Cross X33 w/Campy Veloce
2006 Cervelo Soloist w/Campy Centaur
2004 TiSports titanium road bike w/ Campy Veloce
1998 GT Pulse track bike
Favorite thing about cyclocross:
The people. Coming from road racing, the people--all the people; competitors, organizers, officials, spectators--are what give cyclocross the energy that makes it so welcoming.