That is indeed the reason why the Prestige class items are excluded from Armor Synthesis. You can see a response from Bungie confirming this in this recent post here:
https://www.bungie.net/en/Forum/Post/260003068/0/0/1
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So the 4 cloaks and 2 armor sets that are exactly identical just color swaps are completely different and not the same issue from the 2 leviathan cloaks that are exactly identical just color swaps? What?
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Could you provide some screenshots of these cloaks? I'll pass them along and ask if this is intentional and if it can be changed to be more consistent.
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Hope this link works for ya.
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Perfect, thanks!
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Sure thing it'll take a minute to do so but I'll put the links to them in the replies here.