A few things changed. Some of these you already noticed and your logic is mostly in line with how things worked out this year.
1) 2018 Ascent times were doubled to produce estimated ascent times. Call it a small consolation prize for last year's ascent being cut short.
2) Marathon time is now just Ascent time. So a 2:41 marathon is equivalent to a 2:41 ascent. As I looked at the data from the past few years it was a bit noisy and the trend line was close enough to 1:1 that I just went with it vs the old quadratic equation.
3) We factored in the 2019 GoG/SRTR/BTMR times for everybody again. As usual, the fastest estimated ascent time was used. I can't remember the conversion factors I used off the top of my head (it is on a really big spreadsheet at my house right now). So there may be some odd inversions where you see somebody who qualified with a 3:45 marathon but is seeded into wave 1 because they rocked the BTMR.
4) The Golden Trail Series stacked the 1st wave of the PPM. Normally we would have at most 20 elite runners total and they would all fit in the <99 range along with the previous years award winners and other notable folks. But with almost 50 of them this year (on top of the higher than usual number of recent former winners) they spilled up to bib #120. I then allocated the remaining 80 slots in the 1xx bib range so that there was a 50/50 male/female split in wave 1 when it was all said and done.
The last one is the reason why your estimation was a bit off and the slowest "Estimated Ascent Time" for a male went from 3:12 (or so) in 2018 to 2:57(ish) in 2019. It is also why if you are a male who is accustomed to doing well at these sorts of events in terms of the overall rankings, it is best to just check your ego in at sweat check.
Another side note is that 2018 was a super fast year at the pointy end of the race. We had 5 folks under 3:40 for the first time ever. I was used to sitting at the finish line, cheering on the overall winner, and then having 10 minutes to double check things and grab a bite to eat before the next guy came in. Last year, the first guy came in and then the next 4 were right on top of him and it just got crazy after that.
And for anybody else who read this far, I'd be remiss if I didn't link to an older thread about how your starting wave impacts your overall time:
https://pikespeakmarathon.org/forum/index.php?topic=140.0 
--john