Shimano has been clear over the past few years that the difference between Dura Ace and Ultegra is weight. From a user experience standpoint they are supposed to function identically and I have not seen any real information to conflict this.

I would have to look up the weight difference but for a TT bike I wouldn't say it doesn't equates to a performance gain. So its hard to say what benefits you are trying to outweigh.

Between those two, I would choose the less used and newer bike. I did an Ultegra R8050 Di2 upgrade to my bike last year. I wanted to to find a reason to justify a little extra spend on Dura Ace parts, but it really did not make any sense. The only difference I could find anywhere was weight.

You have to be so careful with second hand gear. The first option worries me if it has been used that much, a lot of triathletes don't take good care of their bikes and you can uncover a lot of issues when you purchase it and get it properly serviced. I would go the newer bike/less well used where possible (granted a well serviced older bike may still be better).
No great difference in ultegra versus dura ace in real world tri conditions, I run a mix anyway on most of my bikes!