In the one remaining answer, there is only one brief mention of Newton, which is, "The problem with Newton's critique is his dependence on a straw-man argument." The answer demonstrates that. However, I wonder if it might be helpful to have a closer look at Newton, to grasp why he wrote so critically of the two scriptures in question.
I asked a question on Christianity Stack about Newton's theology back in September 2020 because of evidence that he had become anti-trinitarian; apparently at the end of his masterly work, Principia Mathematica he indicated his anti-trinitarian stance, even if not clearly. I received some informative answers to my question. Links were given, one showing that Newton wrote in support of a Samuel Clarke who had written in 1712 his arguments against the Trinity doctrine. Also, that Clarke and Newton seemed to have used arguments against the Trinity doctrine used by the Socinian Johann Crell in his De Deo et Ejus Attributis. My question is at Is there a link between Socinianism and Sir Isaac Newton's conclusion to his Principia Mathematica (1687) where he attacks the Trinity doctrine?
This does not tackle specific 'trinitarian' scriptures that Newton argued against, but given his sympathy to the anti-trinitarianism of the Socinian movement some 80 years before Newton, the reasons for his critique of 1 John 5:7 and 1 Timothy 3:16 would be the same reasons promoted by the Socinian movement.
If you could provide a link to An Historical Account of Two Notable Corruptions of Scripture which details Newton's reasons, then the answer to your question would be found there, and perhaps it would show links to Socinianism. There might even be clear evidence that Newton's critiques were just the same as the Socinian's critiques. Given that you seem to know of this essay / article / book, and if you have read it, you would already know the answer to your question. However, if you have only heard of this paper, then the need is to find it, for therein should be Newton's reasons for his critiques.
Only once we know the reasons for Newton's critiques of those two particular scriptures can trinitarians then address their objections to his arguments. As it is, we can only address objections to general critiques against those scriptures. But it is Newton's reasons that you ask trinitarians to object to. His reasons would agree with Socinian reasons, yet the published work, An Historical Account of Two Notable Corruptions of Scripture would be the only way of being totally sure about that.