If anything this assessment is generous. As the article says, it gets better with every new ICE, but I think it needs help from cards which probably don't exist yet - and possibly never will.
Using it blind isn't really an option, so this needs to be combined with some sort of deck-stacking tool to actually get the ICE you want. If there was a way to put cards from HQ (or even Archives) back on top of R&D then there's potential here with Levi University to get exactly the ICE you want; but currently, even with precognition, you're still gambling that there is a suitable ICE near the top of R&D.
Really? I don't think I ever do this as the runner. The only situation that matters is if the runner indexes and sees more than one ICE, what are the chances that he gives you the big scary one that he can't deal with before the small manageable one? Maybe there's a tiny set of fringe cases where the lesser ICE is actually still quite awkward for him and he's confident the Corp has no chance to get the bigger one into play, but almost all of the time I would give him the small ICE first, even before Mutate was a thing. You can't risk the Corp making a big economy boost play and suddenly being able to afford it. If you give him the big one first he might save up to be able to afford to rez it; if you give him the smaller one he's more likely to spend money on that, making the bigger one even less likely later on.
But anyway, this is such a low percentage scenario: the Runner must have Indexing, successfully use it and see multiple ICE before this even becomes a consideration.
OK so the EV of playing mutate in this deck is between $2 - $3.5 - just play Beanstalk Royalties instead.
I'd disagree with this calculation anyway: if you turn a Quandary into a Tollbooth then that's $7 worth of value in ICE, but it's cost you $2 to play Mutate, so your margin is only $5.
But anyway, Mutate isn't about gaining credit value! It needs to be about improving your board position. It needs to turn a dead ICE into something that will either gear-check the runner and/or tax him significantly more than the ICE you're trashing. This means it needs to be reliable, which means it needs to have help - and this is the problem!
Jinteki is already pretty tight for deck space because it needs all the same kinds of things other corps need, plus all the "tricksy hobbitses" stuff to make its traps and guessing games work. OK, so perhaps a deck with Mutate forgoes all the tricks and traps and plays more like a straightforward Glacier. What does it gain? What makes it better than other, similar builds? You have to question why you aren't just playing the same ICE out of Weyland or HB with their superior economies; or Tennin Institute with its Archive traps and Fast Advance tricks.
Defence to Parasite probably isn't much of a thing - more often than not your ICE is dead instantly so you'd never get the chance; but when it's not you have a very small window to execute the mutation - how often will you end up using it blind in this situation?
Knight / Femme / Yog I can see your point about - your ICE has been rendered irrelevant; but you have to guarantee you're replacing it with something relevant or else it's credits down the toilet. So again, Mutate needs help.
Out of position ICE? Again, it's annoying when it happens but Jinteki already have solutions to that: Midori and Tenma Line - yet neither have seen much play.
If I want to play big ICE I'd honestly rather just play more economy and rez them the usual way. The Root will be an excellent economy source for that purpose and Jinteki already have Dedicated Server and good asset economy that's very robust for Replicating Perfection.
Mutate screams "combo" to me. There was an article on here about combos about a year ago (I think Alexfrog wrote it) which basically said that combos are to be avoided unless the individual cards are useful in isolation and/or the combo is a game-winner when it comes off. I would say that Mutate falls a fair way short of fulfilling either criteria. The cards it needs are pretty terrible on their own and even when you pull it off your best case scenario is a rezzed Tollbooth or Archer - which aren't exactly hard to get into play by regular means.