Yes, the Migrant Rights treaty is consistent with national sovereignty, because the nations involved entered into the treaty voluntarily. The treaty still leaves room for each nation to exercise their own rights and make their own decisions, while still acknowledging that migrants have needs and rights that each nation needs to address and respect.
Rights of migrants - this is an issue that is almost exclusively targeted at transferring wealth from Western countries to poorer people. The rights of migrants, barring true abuses of human rights (genocide, torture etc.) are a matter of the country the people are immigrating to and emmigrating from, and have little to do with the UN.