The ministry estimated 921,000 babies will have been born by the end of 2018 —— 25,000 fewer than last year and the lowest number since comparable records began in 1899.

【翻译】卫生部估计，截止到2018年底，中国将有92.1万名婴儿出生——比去年减少2.5万，是1899年有了可比记录以来的最低水平。

本句有两个时间状语：

1. by the end of 2018， 修饰will have been born。

2. since comparable records began in 1899，修饰the lowest number 之前被省略了的谓语has been：and (it has been) the lowest number.

网友的理解正确。但时间状语不能修饰名词，实际是修饰被省略的has been。