After the first time you execute the game, it will create an ini file for your configuration in your "My Documents" folder. Locate and open the "RushEngine.ini" file with Notepad. The file is located in My Games\The Last Remnant\RushGame\Config.
There is a line in RushEngine.ini called:
Change it to "TRUE" (without quotes) and then save the file. You can then change NPC weapons and accessories manually in game, however they will still ask for new equipment and items. If you give them new equipment they might still override the slot without putting it back into inventory like in the normal game.
Suggestion: Give them items they want, but don't give weapons or accessories they ask for. Do it manually so you can keep that equipment for selling or disassembling.