You ask this question, and then immediately go on to talk and showing that you already know the answer.
You either don’t understand the premise, or you do. Pick one.
Organelle upgrades ——> Tissue and organ upgrades.
This is not a new system. This is literally just the same type of thing that is already planned, just scaled up to the next stage.
Literally nothing about this prevents us from having gradual changes. That’s a load of nonsense.
If you are unable to visualize how the upgrade system can allow for gradual change, you have a bigger problem than just how blood is adapted.
Just. Add. Gradual. Stages. Of. Upgrades.
This is not that hard.
Either have many successive unlocks for each trait that get progressively more specialized farther along the chain, or make each trait a slider that requires mutation points to move, like ones that already exist in game.
Forcing the player to create and edit blood cells is inane, for the same reason forcing them to create and edit pain, heat, and pressure receptors would be, all three of which are specialized nerve cells in the skin, that do not need to be directly simulated in game.
The same way the adaptation of blood can be indirectly simulated by upgrades of the heart or equivalent vascular organs, those receptors can be indirectly simulated by upgrades to either integumentary tissues, or the nervous system.
The player simply cannot be expected to create and edit from 100 to over 2,300 different potential cell types in a multicellular organism:
The cells of many tissues and organs can be edited directly from cells, but clearly not all of them. That is a given, and not something you can really argue against.
Therefore, some of these cell types will HAVE to be either thrown out entirely, assumed to exist regardless, or represented in ways that do not require the player to literally manage everything about it like they did in unicell.
You cannot throw out blood, or assume it’s already there, but you can easily simplify it into a function of the system/organ that pumps it.