No, they won't.

Each programme has its own rules regarding earning, and the amount of miles earned in each programme varies.

Topbonus only awards miles on the basis of the rules of the topbonus programme as published on its website. It does not matter whether, for example, Alitalia would offer more, or Etihad would earn less.
Ditto for Alitalia Millemiglia -miles earned in that programme are governed solely by the published rules of Millemiglia - and ditto for Etihad Guest - miles earned in Etihad Guest are determined solely on the published rules for earning within Etihad Guest.

(If the miles earned would always be the same, then there would be no point having three different programmes, with three different names - as to always earn the same would imply that the programmes are the same).

If you go with Airberlin topbonus, you need to check the topbonus earning rules and check the tables for each airline involved (topbonus may give different miles depending on whether you are flying on Alitalia, on Etihad, and on airberlin).

If you go with Alitalia Millemiglia, you need to check the Millemiglia earning rules and check the tables for each airline involved.

If you go with Etihad Guest, you need to check the Etihad Guest earning rules and check the tables for each airline involved.

And while you could, in theory, claim each individual sector in any one of the three different programmes on the basis of which programme gave you the "most" miles for each sector, this would not be recommended. You should strive to consolidate all miles in a single account, in which you can more quickly build up a usable balance, because if you only gradually top up several different programmes in this manner, you will have to wait far, far longer to do anything with the miles - and you should never leave airmiles in your account for too long, because their value declines each time the programmes rules are changed.