I think it's typical that certain repeats are just perceived as more difficult than others even taking into account the various paces and the fact that it about the same amount of SubT work/vs Rest regardless of the session makeup.
Personally the 1K reps w/ 1 minute are my least favorite, and I'm relatively ambivalent about doing 3 to 4k reps w/ 2 minutes. 2K w/ 1 minute tends to be perceived as the "easiest" of the three that I cycle through.
Maybe it's because the 2k rep isn't too long to be a slog combined with only have to do a few of them compare to the 1k rep, but I'm mostly guessing I'm just inclined that way. That session just kind zips by for me.
If you're just starting out though, I would give it a few weeks to find your paces and not read into early fatigue levels too much. There's a building of load over time with this system and the first week or two might feel good at your chosen paces, but you could find it's not so easy when repeating it for the 5th or 6th weeks. The aim is to find the SubT paces that allow you to acquire the volume of time running in that range and the recover for the next session.
I took a bit of time off in January, then started up and made good catch up progress to open the year before getting hurt with a few unrelated activities. It's been an annoying year in that way but I started back up in earnest in May, and with the heat moving in in June, I only finally feel like I've dialed in the paces, rep, and recovery to execute the workouts strongly and not feel banged up week over week over week.
Also, FWIW there was some talk earlier if about folks wondering if they could stuff the 3rd SubT session into the long run. I did that last year on 50 MPW of this method (6E, 1k-SubTs, 6E, 2k-SubTs, 6E, 10-13 miles with about 4 miles of longer SubT work, 6E). I did made progress taking my 10k time from 44 low to 39 mid, so it's definitely possible to make progress that way. My thought process was that I wanted a long run with some faster work, and I also wanted 2 back to back easy days (though I think people were discussing just dropping an easy run and doing 6 days to take a recovery day).
This year I've decided to just keep the long run easy and do a standard 3rd SubT session. Anecdotally, I feel considerably more recovered this year, despite doing a larger percentage of my running SubT. Whether or not that translates into a better time, I guess I'll find out. Not having a long run with some portion of it faster than easy feels like I'm losing a "mental toughness workout" but whatever, it's clearly not absolutely necessary for people to see results.
Anyway, I think I prefer the 3rd SubT to stuffing it into the long run, although it's taking some getting used to doing the long run entirely at easy pace. I've lost more time this year generally so I feel like I started from a lower fitness level, but I'll have a better idea when things finally cool off some time in September.