Fair pros and cons. At either of these institutions, I think it comes down to how hard you're personally willing to work, as I think they offer similar levels of support. I am not personally a huge fan of ATSU's 3 year clinical education model at remote sites, but I have heard that it provides more space/time to strategize for boards, which you seem to be aware of. PNWU has not had great match results recently, has the highest average student indebtedness out of any medical school in the country, and appears to be more interested in expansion (increasing class size to 140 ASAP, and their outcomes suffered) than producing the highest-quality possible physicians. Though, I have heard plenty of positive things from students at that school in terms of being supported (I suspect the faculty that teaches students at that school tend to be nice, caring people, but there's probably some greed in the administration).
I ultimately chose another program, but did have the opportunity to choose between these two, and I think I would have preferred ATSU-SOMA mainly for factors similar to your pros and cons, and the reasons I listed.
Regardless, best of luck to you.