I already had a Dead Messenger Grenade Launcher from the Witch Queen DLC, so when I finished this week's rerun of Vox Obscura, I naturally got a new craftable version with a higher power. However, infusing the original with the new one requires an Upgrade Module despite being the same weapon. This is the only case I've seen where this happens instead of just 1000 Glimmer.
One is craftable while the other isn't so they are technically not the same weapon and don't qualify for the discounted infusion. The same thing occurs when legendary weapons are reissued with new origin traits.