The point of a structured program, IMO, is reputation. If you take classes at a local school and do well, an ADCOM thinks "good job". But if you take classes @ HES and do well, an ADCOM thinks "wow, that's a tough program - great job".
Search on this - plus/minus are easy to find.
Talking about school reputation is just beating a dead horse. If plays such a role during post-bacc, then it would probably play a bigger role as an undergrad since you took more classes. But as many have pointed out, reputation only plays a small role, especially when grades are similar, but this effect is diluted due to the various other variables involved with med school admissions. Since as post-baccs, we do not have majors, and courses will vary among students, programs, and schools, then the level of comparison between post-bacc programs, and applicants becomes less and less comparable. From my perspective, I could have applied to UC Davis' post-bacc program, or even UCSF's post-bacc program. Given their UC status, I would consider them to be a "big name", especially UCSF. Despite being overshadowed by UCSF's name, UCD's post-bacc program is still up to par in terms of successful applicants (>80%).
Really in all honesty, if "difficulty of a program" and the school's name was such a big deal. One might as well do a graduate program (non-SMP) at a reputable school. Surely a biomedical-related MS, or PhD looks better than a year or two at HES? But as we have found out, that is also highly variable in nature.
But I must digress, the topic of this thread is regards to certificate vs. non-certificate earning programs. Not all structured programs result in a certificate. As famous as UCSF is, their post-bacc program does not report granting any certificates, nor do the other UC's, however UC post-bacc programs often report the same >80% success rate (in getting into med school). Therefore, as I stated, it doesn't matter if you get a certificate, however taking a rigorous courseload at any school and doing well is most important. Where you go depends on you the applicant. One must weigh many factors including cost, time, etc.