Yes. So even with 40% survival to 3" you could achieve the goal of 100,000 3" BG. Considering the biologist thought the >3" BG was what was in short supply, keep in mind that 1" to 3" BG are not being consumed by BG (but rather are being consumed by LMB up to about 18"). They can only eat so many so fast so the loss of your supplemental BG will only be the amount the <18" LMB were short relative to consuming ad libitum. It is possible that you will get more surviving than they recommended. You may want to talk with them about whether exceeding 100,000 3" BG per annum is something they would be concerned about. All things considered; I would prefer to have too many smaller BG than not enough 3" BG.
Unless you know something that I don't, how do you know that LMB <18: are eating the small BG?
It's just that I have never known of <18" LMB refusing to eat <3" BG. Why wouldn't they eat them?.
Go re-read the OP's posts. The biologist didn't specify that the LMB were eating the fish according to the OP. You could assume that they were, I am assuming that they are being eaten by another predator other than LMB. If predatory fish were washed in from the creek, what other predatory fish could be living in creeks 50 miles North of Pensacola, FL besides LMB that would eat <3" BG?
As for growing the fish in the pond to transport, I would recommend digging 2 ponds. One, one acre to grow the fingerlings and another that is 1/10 to 1/4 acre to hold the brood fish. After the first spawn, the week after fish abandon the nests post spawn, I would seine out the brood fish from the one acre pond and put them into the 1/10 acre pond to hold until they are needed in the 1 acre pond again. That will do two things. 1) Reduce the predation of the fingerlings by the brood fish and 2) Minimize the fingerling mortality when the fish are moved to the main pond by seining, or if the OP drains the pond via ditch to the main pond, he has to remove the brood fish to have for a 2nd crop that year anyway. He can use a seine with a big enough opening size to only catch the brood fish when removing them.
As for the growth of the BG, I think the OP has enough of a growing season to stock the main pond at least twice per year, each with approximately 50,000 >3" BG. By doing it that way, he doesn't run the risk of running into water quality issues by having too high of a biomass of fish in the pond, and he minimizes <3" fish predation upon stocking. 50,000 3" BG weigh around 950 pounds. He still has to monitor water quality and O2 levels, but he won't be putting all his eggs in one basket so to speak.
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