Benjamin argues metaphysical naturalism is more probable than not from scientific 'facts'. He takes the latent assumption in the scientific method, namely methodological naturalism, as evidence for metaphysical naturalism. Benjamin formulates his argument inductively with probability theory. His argument can be construed in terms of abduction or Bayesian probabilistic confirmation theory. For example,
If observations O then the best explanation of O is theory T.
The internal critique of Ben's worldview offered by Tim, Carlos, Owen and Luke surrounded Ben's epistemology as to justify metaphysical naturalism. The intractable problems identified were as follows:
(1) Ben's empiricism, explicitly or implicitly, commits the logical fallacy affirming the consequent. Moreover, Benjamin failed to explain precisely the conditions in which beliefs are acquired. If he affirms some form of representational realism and/or correspondence theory of truth then there is no independent criteria to confirm any given mental image or belief, in fact, matches with the truth of reality. Of course, then on such an account the problem of Kant's ding an sich (i.e. thing in itself) surfaces itself (there is irony here). A view with all the room needed for skepticism. Perhaps, better put, it has all the necessary ingredients of skepticism.
The problem of induction (deriving a universal from particular examples) was discussed as a decisive feature of any given empirical theory yet Benjamin felt his view was exempt from the problem. He merely asserted induction as a properly basic belief without an account of epistemic justification. Hence, at which point, any belief can simply be asserted as properly basic (e.g. http://www.iep.utm.edu/phen-con/#H4). Still, probability assumes induction. Likewise, probability is predicated on limited, background-relative, data. Such that new data can always skew the results of old data. Thus limited data can revise any given theory by new data. Therefore, any theory dependent upon probability is subject to whole sale revision. Not much security in probability.
(2) Benjamin asserts his particular epistemic theory is self-justifying. That's fine as far as the claim goes. Nevertheless, Benjamin's rationalism, explicitly or implicitly, collapses to either fideism or skepticism (unless, of course, he can show otherwise). Ben attempts, I think unsuccessfully, to evade fideism or skepticism with some form of non-inferential epistemic internalism (e.g. Phenomenological conservativism). But since no criteria of conditions are provided to prefer one particular epistemic theory over another then the selection of any given epistemic theory (including Benjamin's theory) becomes viciously circular (e.g. Armstrong). Benjamin argues if a proposition appears to be true then that is a prima facie reason to believe it is true in the absence of any defeaters. Again, Kant's phenomenal and nomenal world comes back full force with such a view. On such grounds, it seems, we have a prima facie reason to reject Benjamin's epistemic theory, since it appears to be false, in the absence of any evidence to warrant his theory. . However, Benjamin may be able to provide a criteria of conditions to evaluate the virtues of any given epistemic theory and assess what qualifies as a properly basic belief. In which case, Ben would need to show his particular epistemic theory meets the conditions provided (for the truth of any given epistemic theory to render it self-justifying and/or is properly basic) and tease out the philosophical tensions or apparent contradictions between his empiricism, rationalism and Platonism. Further, Ben's epistemic theory prompts more questions: (i) how does Benjamin know reason, in general, or the laws of logic, in particular, aim at truth? (ii) how does he know beliefs aim at truth? (iii) how does Ben know the nature and limits of reason and/or truth? Ben asserts platonic realism as to abstract objects; yet how does abstract objects enforce or impose themselves on particulars?
(3) The discussion on ethics was intriguing. Benjamin affirms moral realism and not moral nihilism. But Benjamin's version of moral realism suffers the same problems as metaphysical Platonism. How does a particular person possess universal moral values and duties? How do these universal moral values and duties interact/relate with particular persons? What is a universal moral law without a moral lawgiver? How does Benjamin's view avoid the naturalistic fallacy (e.g. GE Moore)?
As to Clarkian apologetics, SRR should continue to address the problems leveled against Scripturalism. (e.g. https://useofreason.wordpress.com/2016/08/05/accounting-for-logic-again/)