Yup that is true eligibility is the most imperative phase of our entire application, but no one really knows how the VO works. I have seen innumerable applicants whose eligibility was cleared with criminality and security still untouched, so God knows best.My AOR is before yours and i received a similar reply as yours and said my criminality has been passed rest all not yet started.
Even I assumed that its the eligibility that is scrutinized at first and then another fall accordingly but it's not.
Apparently its the "Eligibility check" for job noc matching which is the most critical.