I am going to go with E on this. But I can't explain why. Just sounds correct.

But I may be wrong.

correct , why prefer "but they are " over "although"

although is changing meaning of the sentence.. IMO

As mentioned, although changes the meaning.

Additionally, Although is an Subordinating Conjuction, which introduces a subordinate clause. Clause should AT LEAST have a Subject and a Verb.

For example : Although I (SUBJECT) hate (VERB) GMAT, I have to study well for GMAT.

Option A.
This is the correct answer. This option carries a comma(,) after 'cousin', unlike other option that had a semicolon after 'cousin'. It is important to know that a semicolon is used to express more of the preceding word. To show that explanation for it still continues.

Option B.
The use of 'although' here is supposed to be used to introduce a clause for concession.
But it's not acting a such here, this renders the option invalid.

Option C.
This option suffers same fate an option A above, the use of although is practical wrong, and a preferred use of 'but are' is the best approach.

Option D.
'Cousin;' the use of a semicolon here is to used to express or expatiate on an element the more. So, if we say the 'Heirloom tomatoes, grown from seeds saved from the previous year, only look less appetizing than their round and red supermarket cousins' the adjectives that preceded the 'cousin' is not for it.

Option E.
This option looks correct but I think it is improper and a tautology to use ; they are'. We already know that 'they' sop there's no point using ' they' again.