To help us out with this idea, please let us know what configurations are the most important to you! There are many different config files and parameters set within, and we are unlikely to do a single sweep of everything – and will more likely tackle one piece at a time.
If you are able to share what parameters you edit in the config file most often, it will help us prioritize the focus. For example, I suspect editing database credentials is more popular than changing the "maintenance idle wait time" for an FME Engine.
We have our configuration files in documentation.
We have made some improvements to the FME Desktop product since this comment was posted. If there are still some more features you would like to see, above what we have available in FME 2019.0, please create a new idea posting!