'the underlying difference' is a correct and usable phrase in written English.
You can use it to refer to the fundamental distinction between two or more things. For example, "The underlying difference between these two pieces of legislation is their approach to taxation."
The underlying difference between Mr. Brooks and Whyte is ideological.
So what is the underlying difference between the two acronyms: ISIS and ISIL?
We confirmed the underlying difference in the TLR4 nucleotide sequence by Sanger sequencing (Extended Data Fig. 5b, c).
Eventually, when the chain of causation is traced in full, the chances are that the underlying difference between polar and tropical octopuses will be in the DNA itself.
Noah Horowitz, in his June 12 Op-Ed article "Your 4-Year-Old Can't Do That," describes the underlying difference between works by great artists and works by children marketed as art prodigies.
Thus, analysis can reveal the underlying difference between dynamically similarly behaving replicators.
What are the underlying differences between sound recording and publishing rights?
Respondents were distributed across all five-residency programs reflecting the underlying differences in residency size within these programs and evenly between all years of residency.
The healing symbolism of the first presidential visit to the site of the first nuclear bombing of a civilian population has overshadowed the underlying differences between Japan and the United States.
This prompted us to investigate further the underlying differences between the two protocols.
Finally, Fisher's Linear Discriminant analysis (FLD) [ 26, 27] was used to visualize the underlying differences between the wild type and the various mutant classes.
