Newton wrote Principia in Latin, not English. Latin being, at the time, the language of what Newton practised, natural philosophy and continuous with theology. There was no such thing as science. Thus, it was perfectly normal for Newton's thought to mature, and the Scholium reflected the progress of his thinking over two decades.

Aside from having to add Latin to the scientific cannon alongside German and English and Russian, the direction in which Newton's thinking evolved is disruptive in the context of contemporary science's self image...none of which is surprising given Kuhn's work.