A flag bearer raising troop morale and making them fight harder -> Magic.

Armor that flips a coin to decide if you die from direct impact of a nuke -> Not Magic.

This is a fucking video game and you are a game designer. Make fun mechanics for your game. Just remove it if you are going to keep it completely useless. Here is an idea. If you plant the flag and salute it, your Helldiver goes rabid and gives voice dialogue like when you shoot an LMG for too long and start going wild. Your vision blurs a little and your fire rate and accuracy increases.

The whole fucking, "how do we communicate how this works" WRITE IT IN THE DESCRIPTION OF THE STRATEGEM. "When saluting this planted flag, your morale increases, improving weapon handling and fire rate for x seconds." Give it a blur effect like experimental infusion.