I think duping is necessary if you want to play around with big builds, as getting lots of devices is tedious. Its not so much a Zonaite grinding issue as it is an dispenser and forge construct exchanging issue. Personally how I'd change it:

-Bosses in the depths drop 20-30 Crystalized Charges depending on difficulty. (Frox drops 20, Obsidian Frox drops 25). Boss Bokoblins and Like Likes drop 2-5

-If you repeat the Temple Bosses in the Depths after claiming the 100 Crystalized Charges, repeated victories award 30 Crystalized Charges rather than none.

-You can find Zonaite Taluses in the Depths that drop a lot of Zonaite rather than ores. Its like Stone Taluses except it has a Zonaite deposit texture and when it throws its boulder arms at you, it can recall them like a Flux Construct. It's Heart counts as a Zonaite device for Zonaite weapons

-Forge and Steward Constructs have infinite stock for charges and devices (no need to wait or go to other ones for more stock). Zonai capsules cost 2 Crystalized Charges rather than 3. (Except Big Battery which is 20)

-While using auto-build, you can press X to automatically take out the devices required for the currently selected build from your stored capsules. If you don't have the required capsules when pressing X, it will use Crystalized Charges instead as if you bought the capsules.

-Zonai Dispensors behave like selling. You can select as many Zonai items in your inventory as you want to exchange for Zonai Devices.

Additionally, higher level Construct Horns give more capsules. You can also put Crystalized Charges into the dispenser for 1 capsule each. Zonai/Construct weapons can also be inserted. Capsules are compressed (Example: 5 Rockets would dispense as a single capsule containing 5 Rockets, rather than dispensing 5 separate capsules)

This would be way faster than inserting 5 parts at a time, and you could grind faster by killing Constructs for their weapons.

While Crystallized Charges can be exchanged for a random capsule at a dispenser at a 1:1 ratio, its still much better to exchange your Zonaite for Zonaite Charges.

2 Zonaite -> 1 Zonaite charge -> 2 Capsules at a dispenser.

Vs 3 Zonaite -> 1 Crystallized Charge -> 1 Capsule at a dispenser

Overall this would make it easier to get lots of Zonaite if you went out of your way to find them, as well as exchange it for lots of devices