As a rank and file employee, I get the idea to say "my kinda sorta work related thing I do outside of work hours is my own property"
As a CTO, that seems weird. All of your energy should be going into your business. If you have time to manage side projects in addition to being a startup CTO, is CTO the right role for you?
Not to say all code you wrote for your entire life now belongs to your current company. But it seems like you have passions and you can now use these at your job. Isn't that the dream setup? Just make sure you are fairly compensated for the gains the company makes, and it should be reasonably fair? Hard to know more without details of what you are talking about...