Did Lincoln's powers as commander-in-chief of the military cover those individuals not under military authority or not in rebellion?

There were loyal Unionists in areas under rebellion whose slaves were freed (particularly after the EP). But the border states and other areas that were firmly in federal control were exempt because the wartime necessity, the actual reason and justification for such radical maneuver, did not exist.

Now, COULD Lincoln have tried some way to free all slaves regardless of the military situation? Perhaps. I'm sure there are ways for someone to interpret the Constitution and the law to find a loophole. But, practically speaking, the president (and Congress) focused the confiscation of property to areas in a military crisis where such confiscation had legal grounds.

You said: "It is a judgement of those congresses abilities t o pass laws and make acts, which they did quite well and without little opposition."

The statement, "the fact it took [Congress] from 1861 until 1866 to end slavery IS inexcusable," is not an assessment of abilities but an assessment of performance. You asserted that the delay in enforcing national abolition was "inexcusable," meaning they SHOULD have done it earlier, not that they simply COULD have done it earlier.

"So the war wasn't about slavery? Thats what I thought. Like I said "Its simple, they could have freed the slaves much earlier if they really wanted to." They didn't want to."

The military conflict was not (at least initially) about slavery, but the sectional conflict leading to secession certainly was. I agree that most people in Congress in the early part of the war had no intention of enacting emancipation. They were concerned with reuniting the Union as it was, especially those from Kentucky, Missouri Maryland and Delaware. Only after the military effort dragged on and slavery was seen as the strength (and potential weakness) of the South, did the administration and Congress formally turn against it in the form of the Confiscation Acts. Such acts helped change the dynamic of the war, as people realized that the Union (even if saved) could not return to its previous status quo. Thus, Northerners increasingly adopted the more radical stance against slavery, deciding that it was best to end slavery as a blow to the Southern war effort (and as punishment), as a moral boost to the Union cause, and as a means of preventing future slaveholding sectional conflict after reunification.

So, I agree that during much of the war, many if not most legislators were not ready or did not want to take the dramatic step of enforcing national emancipation (particularly those of loyal slaveholding states).