Responses to your questions are in bold font.

1. Can we provide in the RFQ for BPA call that BPA holder to provide the technical and cost proposal so we again technically evaluate the BPA holder for BPA Call. Yes. Otherwise, you would have no basis to evaluate offerors for the BPA.
2. if yes, does it mean the BPA holder can be technically acceptable at BPA level and not technically acceptable at BPA Call level? Yes, but only if you permit BPA offerors to propose against a portion of the services to be performed. However, if you are soliciting offerors on an all-or-none basis, it naturally follows that any companies selected for the BPA would be pre-qualified to perform any of the services.
3. This would also mean that we can provide an evaluation criteria for BPA Calls in the BPA. Yes, but by not thoroughly "pre-qualifying" offerors during award of the basic BPA (question 2), you would have to expend the time and effort to perform evaluations for separate calls which should have been performed when awarding the BPA.
4. Can we also have costs (reimbursable cost)  other than fixed price for travel etc. Yes, but not for commercial items (ref. FAR 12.207).
5. Can costs like PPE (in view of COVID-19), utilities, office supplies and equipment included in the loaded rates or any of such cost need to be quoted separately by the contractor. In DOD, guidance was recently issued that contracting officers should account for COVID-related contract costs separately. I don't know if USAID is requiring the same. Overhead (utilities, supplies etc.) should be accounted for in the loaded rates. As such, don't need to be separately proposed. However, they can be subject to Government audit.
6. Finally, can we ask the contractor to provide breakdown of the loaded rates. You can ask the contractor for a breakdown (or at least a general explanation) for the loaded rates, but you need to balance the Government's need to know with the offerors' willingness to expend the time, expense, and effort to do so. If you require specific information relating to proposed overhead rates to determine price reasonableness, you need to include that requirement in the solicitation.