Ditto, also got 15/25 with compliant loadout and all modifiers. Haven't tried again.
Sequence of events in my case:
1. Joined my brother's session via invite; we ran with just the two of us.
2. Chose a frame and weapons from the list. Activated all modifiers.
3. Completed Exterminate; received Blue Archon Shard.
4. I died repeatedly in Alchemy. I abandoned via the prompt on the death screen, which removed me from my brother's party. He aborted the mission separately.
5. Returned to orbiter. Swapped my melee to another valid option, added archon shards to my Warframe, swapped my subsumed ability.
6. Joined my brother's session via invite. Returned to Sanctum Anatomica.
7. Re-entered Deep Archimedea. Loadout was still valid and all modifiers were still checked.
8. Completed Exterminate; received nothing (which is correct, since I'd gotten the one Archon Shard from the failed run).
9. Completed Alchemy; received a Tauforged Crimson Archon Shard (so I must have been at 10 points here).
10. Completed Disruption; received 3x Entrati Lanthorns (which tracks with it showing 15 points when I was done, though I should have had more than that).
I recorded both runs. I'll upload the videos later and edit them in to this post.