The identity is needed by the server. If it's not configured on the server, just set it to some dummy string, but some value is still needed. Otherwise, you'd have to check/get the identity from the network server.
I have not had too many issues with the PyMakr plugin for atom. But I can understand if you do not like that setup. At least with more recent version of the plugin (November is the last I used it heavily), I did not have problems. What I remember annoying me the most was not being able to copy from the REPL.
Yes I use a similar thing for my commercial product. But remember that nodes may miss (due to RF issues, power) the "key change" message and still use the old one.
What I did was to clone the existing device on the server backend but with the new keys. Then when a transmission arrives on the new device (which means the node has updated the keys) the old device is deleted.
If the next transmission still arrives on the old device it means the node has not picked it up so a new key change message is scheduled for retransmission - this is repeated until it's finally picked up.
I never used tools other than ftp and telnet for WiPy and Lopy. Pymakr was unreliable from the first version on and never improved.
When you use FileZilla of FireFtp as ftp client, you can set it up that a double click on the will will open it for editing in our favorite editor and saving stores it back to your device. You can also configure at least FireFTP for auto-conect.
Obviously that causes some flash wearing, in contrast to PyMakr's method to keep files on your PC and load them on-the-fly. If you prefer that method, you can also try Dave Hyland's rshell (https://github.com/dhylands/rshell).