I believe some changes in Sage itself may be the culprit here. I will have to try and dig into it. Sagextras really just took code from an older version of Sage and plugged it in to retain behavior, and @Johnny_Bit did a lot of great work to clean the code up and make it more modern and nice.
Since Sage 8.3.0, after_setup_theme now needs a priority, see https://github.com/roots/soil/commit/82a3fb117e9d338064235ebb29564c7d75be05fc
I’ve updated the plugin to add the priority to after_theme_setup. Kindly try that out and let me know how it works out for you.
Thx very much. I’ve just updated the plugin and it seems to work!