Here is what happened, full story. Purely speculation on my part, of course.
It's July 2013. Pikmin 3 releases for the Wii U.
At some point before, or few months after. The development of Super Mario Maker begins. Before anyone starts, I know how EPD groups work and it's just not like the one EPD group shares the same staff on every game they made. But I know that Shigefumi Hino, Pikmin 3 Director went to work on Maker after Pkmin 3, he also then worked on Maker 2.
So, we are in 2013. Pressumably both Pikmin 4 for the Wii U and Super Mario Maker are in full development.
Fast forward to Spring 2014. the "NX" or Switch if you want is now in full development. Koizumi as a General Producer and Kawamoto as a General Director are brought up to development by Iwata himself.
At this point you may assume that they maybe considered Pikmin for a new hardware at the time but that's not the case since in 2014 Nintendo somewhat thought they could save the Wii U. Remember E3 2014? Zelda, Mario Maker, Splatoon, Star Fox. All of these games were scheduled for release in 2015.
We must now skip to the infamous interview in September 2015. The interview itself was not actually taking place in September tho, it was July of 2015. It was then published 2 months later, but that's irrelevant. The quote itself "it's actually very close to completion". I don't think Miyamoto was actually reffering to it's development or what not, he maybe ment concepts or something, the fact that Miyamoto does not speak much English at all also does not help since his words need to be translated back and many things could be also in translation. But. Do you actually think that the Pikmin 4 could be "close to being done" just 2 years after Pikmin 3 released? They maybe were using some assets and what not but that seems really small development time, even with some EPD10 staff making Super Mario Maker at that time. And we know that Nintendo is sometimes weird with these estimates remember how BOTW went? I know problems with engine and such but they assumed they will release BOTW in just 34 months (January 2013 to roughly November 2015) if that game would be released in 2015.
At this point, when he last reffered to it in 2017 it's safe to say that it was already rebooted, because he talks about "progressing" and "told not to share anything from PR" that just sounds like we will not see it anytime soon. And as I say previously, we don't know when it was rebooted, it could be in 2016, it could be in 2017, it could be in 2018. I don't actually think that it needed to be rebooted multiple time, I just think it was rebooted when Wii U version needed to be scrapped. So somewhere between 2015 - 2016. But that quote from Miyamoto himself is still curious, maybe the game itself was ment to be swan song for the Wii U and could be released in 2016 but then they realized it would not make any sense and since the game was never officially announced for the public it was somewhat fine. Yes, it was announced by press release by NOA and talked in few interviews but aside from that? Nothing, so it was somewhat safe for them to scrap the game for Wii U.
Development of Maker 2 itself probably has not helped much either (again, don't compared the full staff so I don't have the full picture here), but I think it's still relevant. Miyamoto working on Mario Run in probably good chunk of 2016 is also a point, or his theme park involment, and the movie from like 2017 onwards.
TLDR: I think that the development was probably rebooted only once, and that was when they made the change from Wii U to Switch. Other factors also played a role and the game was probably never in full active development till like late 2018 to somewhere in 2019. Remember, it was not until mid 2020 when Pikmin 3 Deluxe released, and year later Bloom was released too. It all makes sense now, it was a preparation for a new title to come, to starting people see Pikmin again when Pikmin 4 comes.