I don't think there's really a "functional gap". All generally useful programming languages including Prolog are imperative "in the end" no matter what the books say, and anyone good at using them will think about the programs imperatively. The language just has "special features" such as ones that go like "try to match this with that and examine each possibility separately". If you try to write Prolog by "describing" the solution instead of thinking about the steps to achieve it, the code will likely not work at all (infinite recursion) or be very inefficient, in spite of being logically correct.
What may look like a "functional gap" may just be the lack of ability for abstract thought, and more correlated with (in)ability to write well structured and generally "nice" code, especially to identify common patterns and create reusable code. Because functional/logical is just an implementation of some abstract pattern that is believed to be useful, and the person may have trouble understanding this pattern just as they would have problems understanding existing abstractions or creating their own abstractions.
I think you're over-simplifying things if you say that not understanding Prolog programs comes down to a "lack of ability for abstract thought". You can think abstractly all you want, that will not help you if you don't know by heart the sometimes arcane rules of setting choice points and binding variables. Those are not things that you can work out on your own, thinking abstractly; those are concrete rules chosen by people over a period of 40 years.
The converse is true, of course: A person that cannot write well structured and "nice" code in other languages won't be able to magically do that in Prolog either.
What may look like a "functional gap" may just be the lack of ability for abstract thought, and more correlated with (in)ability to write well structured and generally "nice" code, especially to identify common patterns and create reusable code. Because functional/logical is just an implementation of some abstract pattern that is believed to be useful, and the person may have trouble understanding this pattern just as they would have problems understanding existing abstractions or creating their own abstractions.