Is there a way to make Atom look more compliant with the elementary's design?
Yes there is. There's a special UI theme called
elementary-light-ui that you can use. The theme was created by one of the main elementary's developers (Cassidy James). To install it, just type in the following command:
apm install elementary-light-ui
After it, just press Ctrl+Shift+P, type
change themes, press Enter and select
elementary-light-ui as your new UI theme.