To understand Lincoln and his cabinet we have to understand that his main goal was to preserve the Union. One of the factors may be that in the beginning his hand was forced to act in such a way that went towards abolition of slavery. Firstly he had to secure the border states, so in the beginning he had to address the issue carefully.

Now at the start of the war you already had The Fugitive Slave Act of 1850 which some general such as Benjamin Butler ignored and claimed that runaway slaves were "contraband of war". That forced Lincoln to publish Confiscation Act of 1861. The Act was first step towards Proclamation. Still Lincoln didn't secure border states, so he proposed first draft of Emancipation like Act that failed, only to be signed by District of Columbia. In 1862 after abolishing slavery in the United States territories (not in States) Lincoln signed Second Confiscation Act or Confiscation Act of 1862 furthering even more rights of slaves in the Union. In September of 1862 Lincoln signed his Preliminary Emancipation of Proclamation that led to Emancipation Proclamation in January of 1863. Now why did Lincoln do this? It is worth noting that Emancipation Proclamations do not regard the Union but Confederacy. The idea was to show that Union still has power over Confederacy and it had to be a big blow that's why Preliminary Proclamation came after Union victory at battle of Antietam.

Lincoln made war be connected with politics so he could cut the power of Confederacy. Lincoln issued Proclamations as a commander-in-chief. Those were military orders because he knew Congress would not approve. I believe that as the Union started winning the war Lincoln wanted to implement more progressive laws. If you look it like this Thirteenth amendment looks as a final blow to the Confederacy and final celebration of Union victory.