Perhaps it would be a good idea to describe briefly the objects or intentions of the two bills and two types of treaties.
The multilateral instrument is an efficient and effective way of modifying the application of existing tax treaties that are currently in force, but it is not itself a bilateral tax treaty between Canada and another country. Rather, it affects the application of those tax treaties whereas this tax convention between Canada and the Republic of Madagascar is itself a bilateral agreement between the two countries. The MLI does not serve to replace the existing tax treaties; rather it is intended to modify and supplement their application.
My colleague can provide more details, but this convention between Canada and Madagascar is not covered by the MLI, which as I noted is largely intended to, in an efficient manner, modify the application of Canada's existing stock of treaties, or the existing worldwide net of treaties, not just Canada's.