Is using only bioluminescent, massive buildings to create the carminite crystal a deliberate choice to make the game last longer?
Besides, massive buildings are wonderfully hand-picked.

I'm not sure I understand your question. What do you mean by "to make the game last longer"?

If a non-bioluminescent assembler is used for the Carminite Crystal, the entire process chain can be completed quickly and easily, right on one planet.

As is the case now
The Carminite Crystal is made in a bioluminescent Enormous Assembly Machine
The Science Package is made from this crystal and an AI module, which also requires it.

Creating anything bioluminescent requires the discovery of the planet Tenebris.

Discovering the planet Tenebris requires the discovery of a cryogenic package, and therefore, Aquilo.

Discovering the planet Aquilo requires exploring the planets Rubia, Arkanis, Tiber, Tellus, Crucible, Hyarion, Arig, and so on.

This begs the question: is this artificial slowdown of progress intended or is it a flaw?

The mod itself doesn't provide any bioluminescent technologies, items, or entities. It also doesn't depend on Tenebris. I think you've encountered some kind of mod conflict, with Tenebris overriding my mod's behavior. My mod is completely playable on Velora. You can land on my planet without any items and complete the mod without any issues.

Cloude help me fix this issue

data-final-fixes.lua

-- Velora/data-final-fixes.lua

local function contains(tbl, value)
for _, v in ipairs(tbl) do
if v == value then return true end
end
return false
end

local function add_categories(machine, cats)
local categories = machine.crafting_categories or {}
for _, cat in ipairs(cats) do
if not contains(categories, cat) then
table.insert(categories, cat)
end
end
machine.crafting_categories = categories
end

-- 1. WSR большие машины получают big-recipe / big-smelting
-- (это уже делается в WhistleStopTweaks.lua через table.insert,
-- так что здесь только подстраховка)

-- 2. Все bioluminescent-* машины получают metallurgy-or-assembling,
-- чтобы крафтить Velora-рецепты (carminite и т.д.),
-- НО не получают big-recipe — они не обязательны для этих рецептов
if mods["tenebris-prime"] then
local velora_categories = {
"metallurgy-or-assembling",
-- добавь сюда другие Velora-категории если нужно
}

for name, machine in pairs(data.raw["assembling-machine"]) do
    if string.find(name, "^bioluminescent%-") then
        add_categories(machine, velora_categories)
    end
end

for name, machine in pairs(data.raw["furnace"]) do
    if string.find(name, "^bioluminescent%-") then
        add_categories(machine, velora_categories)
    end
end

end

-- 3. WSR big-assembler дополнительно получает big-recipe
-- (на случай если WhistleStopTweaks это не сделал до data-final-fixes)
if data.raw["assembling-machine"]["wsr-big-assembler"] then
add_categories(
data.raw["assembling-machine"]["wsr-big-assembler"],
{ "big-recipe", "metallurgy-or-assembling" }
)
end

if data.raw["furnace"]["wsr-big-furnace"] then
add_categories(
data.raw["furnace"]["wsr-big-furnace"],
{ "big-smelting", "metallurgy-or-assembling" }
)
end

It wasn't my mod that added the bioluminescent machines, so it's not my mod that should fix them. Besides, if the author of the bioluminescent machines updates their mod, your fix might break something. Send this code to the person whose mod added the bioluminescent machines.