Crate cover and leaving pup alone

Our 14-week-old puppy sleeps well in his crate about 75% of the time, but only when the crate is completely covered with a blanket (the room is air-conditioned, so he stays cool). In that setup, he can also stay home alone for around 45–60 minutes without any problems.
However, if we remove the cover so he can see out of the crate, he becomes very anxious and starts whining or panicking almost immediately.
We’re wondering if we’re teaching him the wrong things by always covering the crate. Is he actually learning to be comfortable being alone, or is he only coping because he’s in a dark, enclosed space?
Our long-term goal is for him to be able to stay home alone while loose in the house, not to depend on a covered crate forever.
Has anyone experienced something similar? If so, how did you transition from a covered crate to an uncovered crate and eventually to leaving your puppy loose in the house?