That being said, I am curious to know how the cyberware effects the stat increasing implants.
For example, does the int implant still give you increased skill points when you level? The charisma etc implants, do they still count towards perks? For example, animal friend needs 6 charisma, normally I only reach that with the implant. What happens if you remove the implant later after gaining the perk?
Well, I'm answering your question indirectly because I don't really know
First of all, the stat increases are the same as they were before with the original implants. They add a perk, and this perk adds an ability with gives a stat increase. The only difference is that this implant perk isn't applied directly after you buy it (like it used to be since it was directly installed).
So it would probably just behave like, for example, an item that increases a special by +1, or like food that buffs strength.