Hi @Joe,
I think the best way is using code to register post types and meta boxes. Then you can use a version control system like Git to manage your code and deploy to your server. It's much easier and saves you a lot of time if you want to manage multiple websites (even not in a multisite network).
In case of multisite network, I think you can make a must-use plugin to register post types and meta boxes. That way you don't need to activate on all sites in the network.
I think the builder is not very useful here as it requires user input, meaning you have to click-type-click many times to add meta boxes for sites (even with import/export feature). Even though, it's useful if you want to add "extra" meta box for a specific site.
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