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"underlying differences" is a correct and usable phrase in written English.
You can use it when you want to refer to distinct differences or issues that are not readily apparent but still have an effect on the situation. For example, "While the two sides may seem to agree on the surface, underlying differences in their approach to the problem make a lasting solution difficult to achieve."
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Contrasting FMAS characteristics in different study areas reflect underlying differences in agro-ecosystems, aquaculture technologies, farmer livelihoods and markets.
Alternatively, underlying differences among tissues could interact with oncogenic mutations to produce different outcomes.
On seven issues, Catholic Supreme Court justices voted differently from Protestant and Jewish justices, even when taking into account underlying differences in each justice's ideology.
Will similar underlying differences come to the surface as the postwar Iraq develops?
There are underlying differences about our understanding of the bible and of God.
Walls and isolation may diminish overt violence in the short run, but they encourage underlying differences to fester.
These underlying differences, for good and for ill, can now be spelled out for the first time.
Ziedan traces this notion of heresy to underlying differences between Greco-Egyptian and desert Arab cultures and their view of divinities.
Those underlying differences of motive and vision also supply the framework for the series of minor irritating disasters that bring the plot to its climax.
She and Russia's president, Vladimir Putin, agreed to tone down their hostile language, but did not resolve underlying differences.
Dr. Jackson at first tried to tease out underlying differences between vaccinated and unvaccinated elderly people by using medical codes — a numerical shorthand that doctors use to classify and record what is wrong with their patients.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com