The only thing I can think of is to set the font used for each book. When you change the font settings while reading, they are stored for the book and the config file is updated. If you close and reopen the book, it's stored settings are used. If you open a new book, the settings from the config file will be used.
My Kobo Utilities plugin for calibre has a method to take advantage of this. You can use it to set the font settings for the books on the device. So, you could set all books to have the same settings and then let the Pocket articles use what is in the config file. Not ideal, but it should get close to what you want.
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