Which ticket stock is used does not matter at all for mileage accrual. Only the flight number counts. That said, you need to look whether the flights you want can be sold with an AB flight number, meaning that airberlin code-shares those flights. Such an AB-flight can then be issued either by AB or EY, but again, the ticketing does not matter for the mileage accrual.

I believe that in your case you are experiencing first hand that in airberlin's call center right now there are 90% new staff who don't know much about what they are doing. The other 10% don't care much anymore because they have been fired already (effective end of the year). I do not venture to say into which group the agent belonged that you had on the phone.

Ask your TA about the flight number. If an AB-code for the EY flight is available, then don't worry about the ticketing of that AB flight number on EY ticket stock.