There are no municipal-level rental restrictions. 

I've walked through a property with a wholesaler and when I walked in I told him the ceiling height here is a big factor for resale and I can't use the comps he sent me.

If you eventually convert the property to your primary residence and later sell it, the taxes would be prorated based on the ratio of time the property was investment property.These items should be addressed and discussed with your tax and legal counsel to ensure that the exchange is the best course of action given the restrictions and requirements. 

House hacking a duplex can be a great move, and Houston has some awesome spots like The Heights, EaDo, and Spring Branch.

Trustor will not permit any change in any license, restrictive covenant or easement without Lender's prior written consent.Now the practical answer is no one is coming to check on the property most likely, and unless you default no one will likely care.

And I wonder if CCR or HOA can restrict these to protect the values of those homes ? 

You can do less than 20% down (as low as 3.5-5%) if you intend to occupy the home for at least a year.2) There will be an HOA (homeowners association) which restricts rentals, so be sure to read the CC&Rs (governing documents) to ensure that your rental strategy is allowed, even if you intend to live there at first, eventually you'll be transitioning it to an investment property, so this will be important.

Additionally, any existing restrictions at the town level (there are MANY) will be abolished, unless deemed "reasonable" by the state.

You'll also need to avoid environmentally restricted spots, including wetlands, protected habitats, and prime farmland.

Some Other restrictions have been removed.