I don't think the original mod is ever getting updated, so posting this here:
The cost for the MK3 Beacon does not follow Space Age fluid transmutation rules. Vanilla recipes which use Fluoroketone are very explicit in never returning more Hot Fluoroketone than the cold such they consumed. They achieve this by tagging the Hot Fluoroketone as "ignored_by_productivity" for the full amount returned, and typically tag both Hot and Cold as "ignored_by_stats" for the amount of Hot Fluoroketone. This ensures that general stats don't include transmuted Fluoroketone, and also that result can never exceed ingredient.
What this means in practice is that the MK3 Beacon Recipe should look closer to this:
data.raw.recipe["wr-beacon-3"].ingredients = {
{type = "item", name = "wr-beacon-2", amount = 1},
{type = "item", name = "low-density-structure", amount = 20},
{type = "item", name = "quantum-processor", amount = 40},
{type = "fluid", name = "fluoroketone-cold", amount = 40},
{type = "item", name = "refined-concrete", amount = 20,ignored_by_stats = 20}
}
table.insert(data.raw.recipe["wr-beacon-3"].results, {type = "fluid", name = "fluoroketone-hot", amount = 20,ignored_by_stats = 20,ignored_by_productivity = 20})
Suggest having a look, just to keep things consistent with Vanilla functionality.