I have not forgotten that at USA indoor in 2012, Rupp finished 3rd in both the 1500 (behind Manzano & Centrowitz) and 3rd in the 3k (behind Lagat & Lomong). Even though he ended up going to WIC in the 1500 -- because Manzano opted out -- those two races at the 2012 USA indoor championship that you highlight comprise the total of Rupp's USATF championship appearances -- junior and senior -- going all the way back to 2003 -- when he failed to finish high enough to qualify for whatever global championship he was seeking (WYC, WJC, WC, WIC, OG).
From 2003 through 2015, Rupp has lined up for a final 21 times at USATF championship events (junior and senior -- at 1500, 3k, 5k, 10k). In all of those, except USATF junior in 2005, when he was 2nd in the 1500 and no global championship spot was a factor, he has successfully qualified for the global championship he was seeking every time -- except USATF indoors in 2012.
In those 21 finals, he has finished 1st or 2nd 17 times, and of the four 3rd place finishes, two were the 2011 & 2015 5k, where 3rd place was good enough to go to WC (and where he was doubling in the meet in 10k). So, I have not forgotten USATF indoors in 2012, but I have also not forgotten his long and very successful career at USATF championship races. USATF indoors in 2012 (at 1500 and 3k) is his only USATF championship failure in this very long list.
Given all of this, were I betting person, I would not bet against Rupp for one of the top 2 spots in this upcoming USATF indoor 3k. However, the present context is significant: He is 'doubling back' -- so to speak -- from a marathon, and this 3k field is deep and competitive. So, even though I would not bet against him, I would not bet very much on him in this instance. This particular 3k, a month after that marathon, seems a challenge.