Using WP 6.4-beta1-56757 and GB 16.7, the theme provided fonts disappear post uploading a custom font. Here are steps to replicate:

1. Select a block to edit
2. Add the “Font Family”
3. Open the dropdown, and verify all the theme fonts are there
4. Open the Font Library modal
5. Upload and install the new font
6. Go back to edit a block
7. Open the dropdown again, and verify the theme fonts disappear

Video displaying this: