Hi, via Interrail.eu (6€/seat + 2€ booking fee) it is not possible to choose a seat, but you can choose a seat booking a seat via Deutsche Bahn (4,50€/journey). You can book also via NS International (4€/journey + 5€ booking fee - online not possible), but I don’t know if it possible to choose a specific seat. 

Also possible is to go to bahn.com look on their seat plan of the train and book a reservation via Czech Railways cd.cz for 75 CZK/seat (about 3€). There you can’t search from a plan the seat, but you can say that you whant seat xy, and you pay less. 

You go to bahn.com and look for the trip and choose the seat only option. Keep in mind, that on Intercity Amsterdam-Berlin, reservations are only optional. On bahn.com you can look if the train will be full or not.

There should not be a booking fee via NS since you can't book Interrail reservations via their website or ticket machines.

Yes you're correct, but on their website they write:

A seat reservation for an Intercity train or for ICE International costs € 4 per person per one way journey. In addition, a booking fee of € 5 is charged.

https://support-en.nsinternational.com/app/answers/detail/a_id/9325/~/i-already-have-a-ticket-and-want-to-book-a-seat-reservation-as-well.-can-i-do

Thanks for that reference; it's the first time I see this (kind of) secret fee documented somewhere. They don't mention it on the info page about their phone service and reportedly, they may delete the fee when you say that.