Here are some suggestions for improving the Load Order management functionality
Deploy Mods effect on Load Order as a setting: None, All non-native esm files present in Data folder, Only non-native esm files belonging to mods managed by Vortex (it's already capable of detecting whether or not esm files on the list are managed by Vortex, albeit not with 100% accuracy atm)
Purge Mods effect on Load Order as a setting: None, Disable entries for missing esm files, Remove entries for missing esm files
Keeping backups of plugins.txt so that the previous load order can be restored when users Purge & Redeploy (possible means of circumventing the sort issue in the Vortex core app)
Default state of entries added to Load Order as a setting: Enabled, Disabled
Additional means of sorting entries besides drag and drop: Edit entry number, Select entry and use arrow keys/Home/End/PgUp/PgDn, Right-click context menu with Move Up/Down/Top/Bottom options
Means of manually adding/removing entries directly from the Load Order screen: Button added to toolbar that brings up a prompt to type in the name of an esm file to be added, Delete button added to the entry boxes themselves or as part of the aforementioned context menu.