No. He is making the wrong assumption here "that he wouldn't hire me if I wasn't already a founder and not what the company needs". First you ARE a founder- I genuinely do not believe you can't learn the knowledge you needed given how motivated you are. And you are learning. Second, he already admit you are what the company needs (at least during this 3-6 months), so why is he BS you to leave? He's mindset is so wrong for the startup world, just assuming things will take-off and by-then you are not needed anymore. You are desperately needed now; that makes you valuable. Your company probably can't make it to the next milestone in 3-6 months without you, at least it will take longer to hit milestones longer without you. You are valuable, and you feel for the company, just tell him that.
> Is this something that is common?
Yes, but not quite often at this early stage of a startup. I smell some politics of him. Do you two get along well besides tech issues in the company? Since he knows you are still desperately needed now, and he is still making BS about advising you to leave, I can only conclude he probably does not like you (not just in tech realms), and he clearly does not care about the success of the company as much as I do (the company still needs you to be successful at least at this stage of growth).
> Has he overstepped the boundaries?
First thing first, just learn things you need to know fast. You will know when you are making great contributions to the company, and you want that. Don't let your CTO stops you from that. At least when you are working, don't think about the issue with him and grow fast as a coder. I suggest a conversation with him off the work time. If I were you, I would like to know if he had issues with me beyond his doubt in my tech ability.
> It is in my interest however to remain in the company because my equity is vested, the sooner I leave the less I will get in return, apart from my time, and opportunity cost I invested all my personal wealth.
Did you have cliff in your equity vesting? If so have you past the cliff period? I really don't recommend you to leave before all your cliff equity are vested, otherwise you will get next to nothing. Manage to stay with your company at least in the cliff period. Your company wouldn't make this far without you, your company owes you that, and you know through what it should pay you off? Equity. So just manage to get the credit where credit is due.
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May the best luck be with you.