My main thought is that this feature would ideally exist as part of the Editor's GUI, perhaps as a "Sort Styles" dialog accessible via "Tools" or "Options." This could bring up a list of all the styles which can then be rearranged, pinned, etc. according to the user's preferences (the "By-Author Grouping" could be a checkbox).
A GUI to edit this is a "maybe later" feature. Let's operate under the assumption that the initial release of this feature will require editing a text file to make custom configurations to your style order.
If it could only exist as something similar to the existing styles.ini, then this should of course be protected from overwriting during a NeoLemmix update.
It would be purely an editor feature, and no longer tied to NL updates in any way. Styles would contain
their own info about their name, while your personal configuration would be a settings INI file that (at least until a GUI for editing the settings exists) never gets altered or overwritten, only read from. The only exception would be the
editor creating a default config file if none already exists - this config file in turn would have one preset setting, namely, pinning the official styles at the start of the order.