adds an fantastical element to loot, since codex'es are very rare unless you actively go skull mining.
In addition to getting all your normal loot from an codex, you can get treasures.
Think of the way this is handled as the golden hand shadows from persona 4, or the jewel personas from persona 5: Very rare enemies, but defeating one yields an metric ton of loot.

Gold Bars come in stacks of 25, each worth 2,500 supplies.
Elerium Bars (Which cybernetically glow cyan since they are literally "solid intel") come in stacks of 5 and each are worth 1,000 intel.
Gold chests (Look regal, with a key slot) come in stacks of 1 and hold 50 gold bars.
Gold chests need an gold key researched: Gold keys are repeatable research that without any scientists onboard the avenger take 7 days to complete. Gold keys can always be researched at the cost of 1 gold bar.
Elerium Chests (Which glow cyan and have a digital looking numpad) come in stacks of 2, and each chest when unlocked has an set of 25 Elerium Bars.
An elerium decoder is required to open these physical caches made out of solid intel, as they are locked.
Opened and emptied gold chests sell for below half and a quarter their internal stocks value at 16,249 supplies.
Opened and emptied Elerium Chests sell for half of half of half their internal stocks at 6,248 crystals, and 3,124 intel, 1,536 alien alloys.

For 11,111 supplies and 2,555 intel, 2,555 alien alloys and 2,556 elerium crystals, and 768 Alien Alloys you can make an universal skulljack at the proving grounds.

An universal skulljack works on any and all humanoid ADVENT soldiers of AND above that of Advent Officer. Everything from Advent Officer, to shieldbearer, to elite stun lancer are susceptible to Universal Skulljacks.
Universal Skulljacks have infinite uses, but take time to recharge, having an total of a 3 turn cooldown for both skulljacking and skullmining enemy units. You can make multiple however and slot multiple in to have more charges before it needs to cooldown as it is an utility item.

Universal skulljacks shine a metallic 24 karat gold, with holographic tips which are a mix of blue and purple claws. These are meant to offer units an way of hacking, and improving their hacking, when there aren't any mechanical enemies or towers on the battlefield, netting random hack rewards without harm to the user: much like treating the enemy as a workstation or terminal to hack.

Of course: This is all a concept.
You are allowed to adjust the supply and intel count and costs of the chests and bars to balance things out. Even adjusting the price of the universal skulljack is on the table.
The purpose of the bars and chests though is to make the player feel like they've struck gold on a rare enemy however, so making the rewards too small may ruin the enjoyment.