correct, each theme is a package so to install it it needs to go into additional-packages. proton uses theme-switch under the hood (https://github.com/t9md/atom-theme-switch), so to specify themes you'd have to put them in your .proton file like so:

["theme-switch.profiles" ["nucleus-dark-ui atom-dark-fusion-syntax"
                             "atom-material-ui atom-material-syntax"
                             "atom-dark-ui atom-dark-syntax"
                             "atom-light-ui atom-light-syntax"
                             "one-dark-ui one-dark-syntax"
                             "one-light-ui one-light-syntax"]]