English Translation
There is little, if any, difference between the two.
The word-for-word translation makes the word order awkward a bit. I would propose:
あったとしても、両者の相違（そうい） or 差異（さい） or 違い（ちがい）はごくわずかだ。
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相違 is used when there is a gap in opinion between the two.
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差異 and 違い can be used in a wider context. The difference can in opinion, in appearance, in functionality, etc.