Since this email client is open source and used by many developers. Most FE developers like myself use Atom as a preferred editor.
I am having a hard time seeing the difference when switching applications while in high productivity mode.
Is it something we should look into it? I am open to ideas/discussions.

I think changing the icon color would solve the issue. Since the two apps are based on the same technology, it'd still be cool to have the N1 icon "call back" to the Atom icon a bit by having the same basic shape.
I came here to report the same issue. A color change would go a long way at making them more distinctive.
I like this one mentioned in the recent tweet by @nylas:
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Hey folks鈥攖hanks for reporting this. We're definitely considering changing the icon in the future (the one above was actually a mockup by our designer-in-residence @sdewith). We'll see what we can do ;-)
Another request: https://twitter.com/timcameronryan/status/753270254650916864
As a temporary fix, I made nylas.icns.zip and dragged the nylas.icns file onto the icon in the Get Info section.

Most helpful comment
I like this one mentioned in the recent tweet by @nylas:
