I am setting up a woocommerce dokan site. I currently have a theme selected that is compatible with woocommerce but it is not necessarily the one I want to use when I design the pages of my website as I want to do the design aspect of it at the end. What I want to do first is just set up the woocommerce settings, dokan settings, and set up some of the unique functionality for my website that might require more plugins or some code.
My question is after I set up the functionality of the website, can I change my theme to another woocommerce compatible theme while still preserving all the functionality that I set up?

Yes. I’d recommend backing up the site and installing it on Local (https://localwp.com) to test it out without disturbing the live site. If you haven’t launched, then doing it in the live site is fine. You can always switch back to the original theme. Content shouldn’t be affected when changing themes.