The key, I believe, is try to make as little change as possible to the planet, whatever that change should be. So a closed ecosystem is the best option and it fits with our aspirations to leave on other planets as well.

We could live underground and not cut down forests for no reason, let along farming and wood. We should try to develop underground farming to a higher level. Use heat from the core of the planet or from solar panels in the desert to generate electricity that we use for artificial light in our underground farms.
Unlike some people, I actually believe that less organic and natural way of life is the best option for the planet. We should use GMOs to make underground farming more efficient and live our life with our inventions and interfere with nature as little as possible and let it run it's natural course without us.