Last night I was scheduled to do some running intervals and in those cases I usually head off to the track and do Yasso 800s. Coming from a running background speedwork comes in 3 flavors: Track intervals, Hill Repeats, and Fartleks. But I ended up with a curious thought and wanted to mimic an over-under workout with my runs. This is mainly because the last two long endurance runs I’ve done I tried to slightly vary the pace over some 10-15min periods like the TR aerobic workouts and have felt that was a good workout for me so why not try over-unders?
I picked an aggressive 5k pace to be my “over” and an aggressive half-marathon pace to be my “under”. I wasn’t quite sure what kinds of times I wanted with my peaks and valleys, so the first set I tried for 3.5min at the under, with 1.5min at the over. I did that 3 times, taking a good 6min easy jog break in between. Then I did a shorter, 2min under with 1min over 4 times followed by 6min easy jog. Finally I was able to squeak in another 2 sets of the 2min/1min before I needed to head home.
Overall I felt like it was a hard but rewarding workout. I’m curious though if others have taken TR type concepts and implemented them into other disciplines? And why have I never heard of an over-under run workout?
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Sort of, but the other way around. I see TR as implementing what swimming has had for a long time: structured workouts. This includes the over-unders, steady-state, VO2, varying the rest for the effect, etc. Though there’s no power meter, there’s a fixed distance (25yd, 25m, 50m) to execute over and over (and over and over 
) at varying intensities, across varying distances, with varying rest times, etc. and mix and matching them depending on desired result. (Add in different strokes for more variability.)
As far as over-under run workouts, there the Monaghetti format, fartleks as you mentioned (though that’s more randomized, which highlights your point), and the ability to use track work to achieve the same. I’ve not seen that much but I have. But, to your point, there seems to be plenty of room, or rather absence of recommendations, for over-unders in runs.
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Usually called change-of-pace/alternating tempo runs. They are used in training but usually in running there is only so much intensity you can do before you break up. Hence, the standard 20 min threshold runs or 1 (2) mile repeats and/or longer uptempo runs are mostly good enough combined with fartleks and faster VO2Max repeats.
Also, I think over-unders are more race specific in cycling while threshold runs are more race specific in running (10k and half marathons specifically).
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As far as I can tell, the (Jack Daniel) sort-of-equivalent of FTP is Tempo - a pace you can maintain for 25-30 minutes (but then he uses your 10k pace, which for sure is longer for me than 30 mins, but whatever). Daniel has Tempo runs where you do 20 minutes of Tempo, broken into either 4x5min, 1min recovery, or 2x10min, or 1x20min. That’s pretty similar to the “threshold” TR workouts (and feels the same as well). An over-under would them be blocks of 5-10 mins at 10k/Tempo pace -5%, with 1 min intervals at 10k/Tempo + 5%. This would be “tighter” than your half/5k method, keeping the pace closer. One important point of over-unders is to keep the unders as high as possible, so that you learn to recover in the narrow gap between that pace and your threshold.
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I’ve heard of something similar called ‘in and outs’ by a friend who is triathlon coach. He is of international running pedigree and suggested some workouts when I was training for a half-marathon back in those heady days when we could race 
His suggestion was: warm up, then 16km as 8x(1k @ Target HM Pace, 1k @ HM pace + 30s), cool down. It was a great workout and while HM Pace + 30s is by no means slow it really teaches you to recover well at a higher pace.
Like TR, I think the trick with these workouts would be knowing what is sensible and sustainable for run pace. E.g. whilst it might be possible to do 20mins of VO2 pace work broken up over an hour, it is sensible and sustainable or would it be a Joe Friel-esque ‘breakthrough’ workout that you done sporadically. You sound like an experienced runner so you’ll know what your body can handle. Lately I’ve seen some experienced runners on Strava talk about intervals with ‘floats’, but their pace was pretty close to the goal pace for the intervals so it looked really hard sessions.
I could see it working well for marathon training e.g. 16miles as 8x(1mile @ MP-15s, 1mile @ MP+15s). I wonder if when you get down to 5k and 10k it would be too intense. Brad Hudson’s book ‘Run Faster’ had some interesting workouts in it, one being 60mins as 30x(1min @10k pace, 1min easy) - 30mins at 10k pace with plenty of rest was a great way of preparing the body for the intensity without it accumulating too quickly.
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