This is exactly why I was instead usinga Nested Vault for obsidian publish
But this is a cleaner solution to avoid messing with nested vaults.
If a sub-folder is selected for publishing, the left side pane (where the files are displayed) looks empty, until one toggles the folder to reveal the notes inside of it.
I like the idea of making the sub-folder a first level folder in obsidian publsih like @lizardmenfromspace described
I’d also be okay with adding the option to expand everything inside that sub-folder so that notes aren’t hiden by default