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The phrase "are indeed different" is correct and usable in written English.
It can be used to emphasize the distinction between two or more subjects or concepts.
Example: "While both theories have their merits, they are indeed different in their fundamental approaches to the problem."
Alternatives: "are certainly different" or "are truly different".
Dictionary
are indeed different
adverb
Truly; in fact; actually.
Exact(54)
This is shown in the right panel of Figure 2. Wilcoxon tests show that the means of these distributions are indeed different, with an estimated difference in a 95% confidence interval of 0.257 ± 0.032 for English, 0.167 ± 0.017 for German, and 0.287 ± 0.035 for Spanish.
JB These are indeed different issues, but they're closely related.
And the rich are indeed different -- they have always spent.
To demonstrate empirically that sensing and perceiving are indeed different, however, is quite another matter.
The participating companies are indeed different from one another in style and focus, and some are even interesting.
And at first glance, some of its initiatives are indeed different from those of Travelocity and Expedia.
Similar(5)
"She is, indeed, different".
Baking is indeed different from cooking.
Mr. Alagna is delighted that this "Tosca" is indeed different.
The country was indeed different after 12 years of Mrs Thatcher.
That is risky: Brazil is indeed different from Argentina, but outsiders may not realise that.
More suggestions(19)
are undoubtedly different
are quite different
are absolutely different
are genuinely different
are admittedly different
are definitely different
are actually different
are indeed various
are indeed distinct
are indeed other
are indeed several
are obviously different
are furthermore different
are truly different
are indeed distinctive
are even different
are given different
were really different
are really different
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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