Developing for an android device currently but I want to see what the performance is like of a particular functionality. I'm currently running the PhoneGap server on my PC and then connecting it to my phone device via the PhoneGap Developer App. I'm not actually sure how it's working in the backend, is this the same as if the app was running purely on my phone in terms of testing the performance of the functionality (which is pure JS)? Or is there another way to move the app to my device so I can test it?
The best test is building your app using either the CLI or PhoneGap Build and then running it on your device.
Using PhoneGap Developer app can give you an idea of performance, but only if you aren't planning on using an alternate web view in your app. But you should use an alternate web view because the system web view varies a bit (especially on older devices). See cordova-plugin-crosswalk-webview. In that case, PGDev may not be able to tell you much about the performance, since it doesn't use the the crosswalk webview.
Also, there can be some funky edge cases with the PGDev app, so if something isn't working like you expect, you'll want to cut an actual build anyway.