Up to flipping the direction of the duplication glyph, this should be the only viable layout for 42 area or less. Unless I made a mistake, or you do something weird with wrong bonds.

Figuring out the assembly order was a nice puzzle:

First, we perform 4 duplications
Next, the 6 atom segment at lower right
Next, the 9 atom segment at top
Next, the 4 atom segment at lower left
Next, attach the last 2 lone atoms to the lower right segment
Finally, the last bond

Optimizing for cycles was less nice. There are up to 10 different fragments on the game board at any time and figuring out where they go and what order to move them in requires keeping the whole solution in your head.

I did most of my solving on paper, with some help from the plastic hex pieces I posted in the discord. The only change I made after the first version was 6p-ing it to save 5 cycles.