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Некоторая предыстория тут и тут.
Решение лежало на поверхности. Как и я. Последние полтора года. Извините.
NOTE: Фикс добавлен по принципу беглого патча. Значение длины \eqindent должно быть уточнено, а исправление протестировано на тексте с множеством включных формул различной высоты.
PS1. Хотел приложить текст для теста, но уже отправил сообщение.
PS2. Да прибудет с вами lipsum и showframe.