I flew PDX to AMS in early June and arrived 3 hours early for a 1:30 p.m. flight and had way too much time, no line at TSA (I have PreCheck but my travel companion did not - we both used the regular line and it took 4 minutes).
I've flown the 6 a.m. ATL flight multiple times and you should be ok arriving right when the counters open at 4. I've stayed at Country Inn and Suites near airport for early flights and it was comfortable and they have a shuttle. If you're able, check in online ahead of time, but if you're needing to show proof of vaccination for an international flight, it's possible you'll still have to engage with desk staff. None of my FlyReady info seemed to be noticed when we checked in at PDX (but it was on my return from Europe, weird). The ATL Delta flight leaves from D gates. Since the airport is under construction they have two dedicated TSA checks (one for A/B and one for D/E - no longer able to get between the terminals) so make sure you go to the right one. And after security there is a pretty long round about hallway passage to get to the gates - but even then it only adds 5 minutes to your walking time. If you're early check out the new E terminal and the hidden room at the Tender Loving Empire store, where they have a side room with the old PDX carpet. Hopefully you have plenty of connection time in Atlanta as that's where my travel woes have occurred in the past.
Sorry can't answer the question about Athens, but you might want to check the ongoing thread related to Amsterdam airport - I personally had no insanity but that was unusual. https://community.ricksteves.com/travel-forum/netherlands/schiphol-is-still-a-mess
FWIW if you are returning to PDX from Amsterdam, I did have about a 25 minute wait at PDX immigration which was very slow compared to prior returns. If you need to, use the bathroom before you get in line to chat with passport control (nice greeters were suggesting this while we waited in line). After going through passport control, you have to take a shuttle bus from the arrival gate way out around the the end of D terminal and then on to baggage claim (carousel 10). There was a bit of a wait for the shuttle. Total arrival process took about 40 minutes (in 2019 it was about 10). More info here.