Lincoln had constitutional/legal authority to suppress rebellions.
Emancipation was an act of war against Confederates.
States & regions loyal to the Union remained under Constitutional protections until ratification of the 13th amendment.
Lincoln behaved as if the States were out of the Union for the purpose of freeing slaves in areas he didn't control, and then he behaved as if the States were still in the Union to claim jurisdiction over them in every other way.