Eric,
There is documentation on the type of custom applications that are supported and also on custom application created at:
http://www.multitech.net/developer/software/aep/creating-a-custom-application/
You can run your own node.js app on the AEP gateway or a Python app. The only catch is that you have to have an SD card installed on the AEP. Follow the guidelines for creating a custom application at the URL above and you can create custom applications. There are even a few example custom applications at the bottom of the main page on creating custom apps. The examples are node.js, Python, and a binary application using Boost.
The Partial Configuration feature supports the capability to create a custom configuration where you edit a limited number of configuration values (configuration of all values on Conduit is not supported). You do this on DeviceHQ, and then push the configuration to a Conduit using the Remote Management feature. Using this feature will require you to have created an account on DeviceHQ, and enabled Remote Management on your Conduit.
Jeff