IMPORTANT: SEE EDITS BELOW(*)

TL;DR

LGD is only 12% more efficient per energy than ELT. If you had to give up a bonus unit to run LGD, you (*) made a mistake if you had less than 375% bonus to begin with. However, if you had more than that bonus, you are fine as long as you sacrificed only a 50% unit.

Data

Here are the highlights:

The ratio of LGD/ELT in terms of Energy Per Run is 1.12, which is only 12% greater.

What This Means

Because LGD costs 60% more NRG than ELT and they have approximately the same base flower rate per NRG, the bonus rates should also be 60% more in LGD than ELT.

What the data shows is that the expected bonus per run in LGD is 103% more than ELT. However what we want is the total flowers per run, not just the bonus. We add 425 to the ELT bonus and 685 to the LGD bonus to get the actual expected flowers per run. This means the actual flowers per run is only 79% greater in LGD than ELT.

Because the NRG per run is 60% greater in LGD than ELT and our actual flowers per run is 79% greater in LGD, there is a preference to running LGD by (1.79/1.6) ~ 1.12 or 12%

Here's The Catch

If you ran LGD, you may have needed to sacrifice a bonus unit to get a chaining partner. Since LGD is 12% more efficient than ELT, you can only afford to sacrifice 11% of your TOTAL (*) flowers per run to get an equivalent flower rate (1.12x = 1, x = 0.89 = 1 - 0.11).

For example(*):
If you run ELT with a 200% bonus, you are earning on average 2223.51 flowers per run (200% bonus 100% normal) and 88.94 flowers per NRG. If you sacrifice a 50% unit to run LGD you are now earning on average 3318.75 flowers per run and 82.97 flowers per NRG. You've sacrificed 25% of your bonus, 20% of your total flowers per run, and are behind 6.7% in efficiency.

Here's some numbers to give you a sense of the efficiency of ELT vs. LGD if you choose to sacrifice a bonus unit.

According to the above table, the only time sacrificing a bonus unit to run LGD is worth it is if you have a 375% or higher bonus and choose to give up 50% of it to run LGD. Otherwise, the lost bonus won't be made up by a 12% increase in efficiency.

Note: 375% - 50% is where the two difficulties break even.

Additional Notes/Conclusion

Here are the survey results. There were around 130 total submissions and over 10000 total runs to work with.

As for how I adjusted to account for people's first few runs of ELT (that 60 pineapple kills for LGD farmers), I simply found the approximate rate of Pineapple spawns in ELT, which was 1 in 8, and assumed that if 60 Pineapples were killed, 480 ELT runs were held. I also looked at the ratio between Pineapples and Uratan Yensa in ELT, approximately 1 to 2, and removed twice as many Uratan Yensa (120) as Pineapples.

As for the conclusion, (*) it seems I overestimated the amount of bonus you need in order to run LGD efficiently. You only need 375% and to give up 50% for it to be worth it. Thanks to /u/Myskital for catching the errors.

Please let me know if I've made any (other) math errors. If you have any questions or comments, don't hesitate to reply below.