Summary

@McJty has espoused a desire to see people design Endergenic generator setups that involve multiple pearls running simultaneously, but the current mechanics make this a generally undesirable proposition, since it adds complexity without adding any tangible benefit. It's simpler and more efficient to make multiple separate generators and fiddle the timing so that they look like they are linked than to make one large one.
Currently there is no functional (power) difference between 2 generators, each running a single pearl with a 12-tick cycle time and a single generator running 2 pearls 12-ticks offset in a 24-tick cycle. The latter is much more finicky to build correctly, though.

One relatively simple solution would be to assign each active pearl in the system a unique id and then provide a modest power scalar (e.g. up to 2x, like most of the current factors) for receiving a pearl that the generator has seen before, but not recently. This could either be measured in (A) ticks, or in (B) pearls (e.g. the generator last saw this particular pearl 3 pearls ago).

Option A

A generator running a single pearl at the currently optimal 12-tick cycle time (using 12 generators, for ease of math) would retain a scale factor of 1x, and would continue to (ignoring the pearl age factor), generate 12800 RF/t.
A generator running a single pearl but with a 24-tick cycle time (using 24 generators, again, for ease of math) might have a scale factor of 1.2x and therefore generate 12800*1.2 = 15360 RF/t. Taking advantage of the 12 idle ticks to run a second pearl however, would double this expected output to 30720 RF/t.
Option A has the possible consequence of encouraging >1-tick spacing between generators, since longer gaps allow a longer cycle time per generator.

Option B (same result, different method)

A generator running a single pearl at the currently optimal 12-tick cycle time (using 12 generators, for ease of math) would retain a scale factor of 1x, and would continue to (ignoring the pearl age factor), generate 12800 RF/t.
A generator running two pearls with a 24-tick cycle (using 24 generators) might have a scale factor of 1.2x (for having seen one other pearl in between), and therefore generate 30720 RF/t.
Option B explicitly requires multiple simultaneous pearls in order to receive a benefit in the total energy production per pearl.