I don't think their motivation is to exclude eligible candidates. I think they believe that there were ineligible candidates taking the exam and they don't have the manpower to audit those candidates between application and certification. So, now they are asking for more proof of eligibility instead of just taking your word for it.
I think your MD example kind of proves my point. BPS certification isn't supposed to be the minimal competency. That's the NAPLEX. If BCPS becomes minimal competency then I think something else will come to supplant it. For MD's it is the sheer number of available board certifications. That's the direction I think we are headed. Soon, I think that we will see more specific certifications that do what BCPS used to do. Board certification in internal medicine pharmacy or something like that. We already have geriatric pharmacy certification.