The official regulations for the proposed Malta Permanent Residence Program (MPRP) are expected to be published in the coming days and will provide more clarity. However, during the Malta Residence and Visa Agency's briefing last January, Parliamentary Secretary for Citizenship and Communities Alex Muscat mentioned that a route to citizenship after becoming a resident of Malta under the proposed MPRP is being considered, and it is a future possibility. However, no further information on this has since been released. Therefore, as it currently stands and as you have correctly stated, the only option to become naturalized as a citizen of Malta (by investment) after becoming a resident under the MPRP is to apply under Malta's Granting of citizenship for Exceptional Services Regulations. It is to be noted that should you be spending most of your time in Malta once you have become resident under the MPRP, you will eventually become eligible to apply for Maltese citizenship by naturalization on the basis of residence in Malta. In order to submit such an application (amongst other criteria), you would need to prove that you have resided in Malta throughout the 12 months immediately preceding the date of application, and that you have resided in Malta for an aggregate period of a minimum of 4 years, during the 6 years preceding the aforementioned 12-month period. I stress that satisfying such requirements merely gives rise to eligibility to apply and, in practice, applicants who are naturalized under this option would have been residing in Malta for a much longer period.
