I think your idea of stocking enumerated fry into the 1 acre pond for grow-out will work. Caveat is whether 1/10 acre fry pond will produce 50,000 fry per cycle. IMO, the harvest should come out when the standing weight exceeds your estimate. Not all BG will be 3" but the average should be that. This approach will allow him to prep the grow out pond for another cycle at the soonest possible time.
I read the OPs post several times and I felt there were a lot of holes. I do think 10 people could have read it and come away with 10 impressions as to what the biologist was thinking and why that number was selected and to what purpose the supplement is for (eg food for a target sized fish or to strengthen very weak adult BG population). I thought there were several red flags that I will list below.
1. The water is 4 years from stocking. Dang, if I had a nickel for every lamentation posted here around that mark in time ... I would have a few dollars ... I think. So I did wonder if what is happening is just the effects of recruitment and the larger sizes of the original stocking.
2. It seemed to me that the biologist's explanation for lack of forage was that predators entered the pond and cleaned them all out and then exited (left) the pond. The OP didn't say there was a colonization of predators from the creek. Pretty handy "it depends" explanation for why the fish are so lean and not growing. The cost of such a supplement probably ranges between 30 and 40 thousand dollars if purchased (maybe more).
If the original LMB stocked in the OPs pond had grown by ad-libitum feeding, he would have examples of 10 lbs LMB presently. The number of the original stocking would now be diminished to have successfully reached that goal.
The prescribed supplement is for 2000 lbs of BG (in a 45 acre lake 44 lbs per acre). In a 45 acre lake with 60 lbs LMB/acre; the amount of consumption required for maintenance is 372 lbs per acre. The supplement is a minor fraction of that. There will be a benefit but probably less than the OP is anticipating.
The 1/10+ acre pond is for the adults to be placed, the 1 ac pond is to grow out the fry that were hatched there. So, depending on the depth of the 1 ac grow out pond that would determine the pounds per acre foot. But the 950# per surface acre should be pretty safe to grow assuming feeding and aeration.