Yaar
I am just interpreting the notes , I am not expert
.
When they start checking eligibility is not sure .
Eligibility check is of Two rounds - by a Junior VO and later VO. I guess once Junior VO assess the application to be eligible MR is received .
Coming to your question , To me after MR is requested/done/uploaded and before RPRF request if Application is rejected which takes around (7-8) months ,The reason could be to me if Senior VO is not satisfied by the eligibility assessment and the recommendation provided to him by junior VO.
If you get MR and RPRF together no way you can be rejected due to Eligibility .
This is all my understanding , no "Pathar ki Lakker" ;D