I don't think that studing chemistry (I like to think about alchemy as a precursor of chemistry) or theology should be stigmatized. I understand that it was just an example to support the core idea of the article, but it still leaves a bad taste.
So yes, in modern times, theology and alchemy has the same scientific value: none
You're limiting knowledge to the hard sciences.
That kind of thinking is not scientific, but merely Scientism.
You're also ruling out many scientific domains, e.g. history which operates according to the historical method.
Theology (in the original Christian sense of the word) stands on the historical method. It's interested primarily in those historical events from which we can learn about God. If Jesus is not historical, if God has not acted in history, then there's nothing to know about God, and there's no such thing as Theology.
But that is different to the "observe", "measure", rinse-and-repeat methodology which is commonly understood as the scientific method.
The methods by which one studies physics and history are different, but history is no less scientific, and it falls within the sciences, as does theology since it depends on the historical method.
Theology cannot argue or learn anything about God for which there is no historical basis.
I have nothing against theology as a hobby or religious pursuit, but at some point we have to say "the well is dry" and admit that there is no grounds for spending public funds on it. Specifically: the only payback we can expect lies in the student's personal religious experience.
Sure, maybe he just worked less hard on theology+chemistry, or he wasn't good at those topics, but what seems more likely is that there were no useful discoveries to be made there at the time given the tools + world context Newton had.