Yes, you seem to have it all correct.

You can deactivate the travel dates until you are 100% that you are travelling as each day cannot be deactivated once it starts at midnight. I know your plans are fixed but situations do happen.

You only need to arrive early enough to find your train, if walking I would say giving yourself 15 minutes for getting to the platform is more than enough, obviously connecting from other transport you should allow an extra margin for delays. There is limited or no catering on that train from Amsterdam to Berlin so stock up before boarding.

Some places such as Amsterdam have barriers to enter the station, scan your pass QR code or if that doesn’t work show it to the gate attendants, others such as Germany are fully open, no checks at all to board.

There are no fixed borders within the Schengen area of Europe but you may occasionally see spot checks on trains, very unlikely on those routes though.

Reservations are complicated, this page gives a good guide for most places in case you still have some planning to do.

https://www.seat61.com/interrail-and-eurail-reservations.htm