I think what happened was that when Atom was inside he was drawn by a background guy:

When he broke through the window, he was still drawn by the same guy, but the foreground guy drew the breaking window and not wanting to have another guy draw him in front of the window that was already part of the foreground, they just left him in the background:

In other words, the area of the window that is broken and missing was completely transparent. Notice how the break very conveniently is so far toward the left of that pane that is is cleanly broken right along the edge of the frame. The other panes were still drawn by the FG guy, who was too busy or whatever to make a transparency that matched Atom's outline.

Therefore, Atom who was drawn by the background guy, & hence, in the background, is clearly seen in that area. However, I see an inconsistency to this theory in the part of him that overlays the window frame. His front peak & palm of his hand do not seem blurred. On the other hand, it is quite clear that only that one panel of glass had any transparency in it.

Now that part of him is in the foreground (has the house as the apparent background, but it is really drawn by the foreground artist), while the rest in in front of blue sky, only that part that overlaps the house is clearly weird. However, if you look at his the part of him in front of the sky, it seems oddly fuzzy. The sky & the outside of the house were drawn by the FG guy, while both Atom, & everything inside the house was drawn by the BG guy.

Rather than creating a foreground with a transparent part that fit Atom's outline, they just made it semitransparent.