If it makes things easier, I have no issue with not making this distinction.
The way I would suggest wording the feature to make implementation easier: each bio process type gets a speed bonus based on how many other processes there are. So for example if the player has just glucolysis: 2 and iron chemilthosomething: 5, the bonuses are 2/7 and 5/7 for the processes. Then naturally if you throw in some unrelated part then the bonuses fall to 2/8 and 5/8.
This will be much more simple to make and doesn’t cause configuration headaches like “no wait that one process in that one organelle shouldn’t be allowed to get a bonus”.
This as a whole would be a problem though, because it breaks part of the system. If you only compare the number of processes, then you only calculate specialisation for cell parts that have processes. Throwing in pili, flagella and cilia would not decrease the efficiency bonus for chemosynthesis for example. That removes the need for separating process cells from for example flagella cells.
That’s why I think the basis for the calculation of the bonus needs to be ratio of the cell parts themselves, not only looking at the process overview.
I don’t know if in that case “40% of the cell is chemosynthesising proteins, so boost all processes from chemosynthesising proteins” is still easier to implement than "“40% of the cell is chemosynthesising proteins, so boost (manually assigned) the chemosynthesis process”. If the former is still easier, I would agree with doing that.