In general look at AP for sustained blocks as described above when thinking about FTP training benefit. Then look at what dynamic system or fitness component is addressed by any non-isopower efforts. (or vice versa depending on your priorities for the workout)
For instance a common over/under interval might be something like a repeating set of 2 minutes at 90% of FTP followed by 2 minutes at 110% repeated for say 20 minutes. The AP for that interval would be right at FTP but the dynamics of the interval would target lactate tolerance and clearing or the ability to tolerate those harder pushes and then recover in motion.
Similarly a micro-interval workout I like to use is something I call Tempo with a Twist and there are different ways to do it, but a common one is two minutes at 85% of FTP or so followed by a rapid leg speed acceleration for ten seconds then right back to 85% until the next two minute point rolls around (so really a minute fifty at base pace and then a ten second burst). The bursts are too short to really pace but these usually work out to AP around 90% of FTP or right on the lower edge of L4 but the dynamics emphasize rapid muscular recruitment and accelerations. These or variations on them can be used to focus on things like crits and punchy road racing but still have an FTP and sustained power benefit.
And a real nice cyclocross workout is a set of 30x30x30s with a triangular course, usually on a hill. Run one leg with a shouldered bike, ride one leg and coast one leg for roughly a minute and a half per lap. Do one leg all out, Tempo on one leg and recover on the coasting leg. Usually works out to SST/L4 for the overall AP and mimics the bursty demands of cross racing as well as providing some skills work while tired with the dismounting, shouldering, and remounting again and again.
Whether any of these are 'better' for purely raising FTP is debatable and there's not a lot of science proving it one way or another but if you do them for other reasons like breaking up boredom on the trainer of to prepare for more dynamic events they can be very useful.
Yeah, part of that looks 'pull up' but mostly I think these guys go way out of their way to try to keep things interesting. It's really hard to sell a stock 2x20 L4 program, not much to it just ride solid pace for what seems like a long time, rest and do it again. It's hard to say if their stuff is as effective or perhaps even better in some respects (like the dynamic stuff above) but if it keeps you interested and keeps you on track especially while indoors on the trainer then it's probably a decent thing to do. A lot of folks really like their program so I'd say if it works for you then go with it. Personally I tend to either do steady iso-power work or I do dynamic work with a specific goal in mind like emulating the demands of crits or cross or certain expected racing situations like a race with a series of one minute sprinter's hills in close succession.
-Dave
