A far better place than the generation transaction (which I assume means coinbase transaction?) is the last transaction in the block. That allows you to save, on average, half of the hashes in the Merkle tree.

On Tue, Dec 8, 2015 at 11:55 PM, Justus Ranvier via bitcoin-dev <bitcoin-dev@lists.linuxfoundation.org> wrote:

On 12/08/2015 09:12 AM, Gavin Andresen via bitcoin-dev wrote:
> Stuffing the segwitness merkle tree in the coinbase

If such a change is going to be deployed via a soft fork instead of a
hard fork, then the coinbase is the worst place to put the segwitness
merkle root.

Instead, put it in the first output of the generation transaction as an
OP_RETURN script.

This is a better pattern because coinbase space is limited while output
space is not. The next time there's a good reason to tie another merkle
tree to a block, that proposal can be designated for the second output
of the generation transaction.

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