Cutting through the rubbish, here is where this comes down:

1. The CSR and supervisor were both correct. But, the supervisor cut OP significant slack by waiving the $200 change fee for discounted domestic tickets. Under the no good deed goes unpunished, OP now rants against the people who cut the slack.

2. This was clearly two one-way tix and thus not a connection, but rather simply two separate itineraries. The MCT is for connections and only reflects a carrier's willingness to accept the risk of rebooking. Here, if OP did not show for his xSEA flight, his reservation was subject to cancellation just as if he had started out at SEA that day. While it is possible that had he asked for a reroute on arrival at SEA, he would have been granted one, that's not how phone agents work. Nor should they.

3. OP tried to SDC, but was told that it was not available on his xSEA. As OP certainly knows, SDC requires that seats be available in the fare bucket on which he was ticketed. The fact that there may have been seats available in general is meaningless. Changing when there are seats but not in your fare bucket costs $200 (and isn't waived for elites). That's what OP was told and then got waived.

4. For all the blow-by-blow quoted by OP, OP doesn't provide the reason for the delay. Likely, "it's not our fault" means WX, ATC or something beyond DL's control. Indeed, it means that it's "not our fault".

5. The "administrative fee" was likely the $50 fee for taking over the reservation from Expedia and some small fare difference. OP should understand that some air carriers would flat out refuse to touch the reservation before the first segment is flown and would have shipped OP off to Expedia where the $200 change fee could not have been waived. Again, another favor by the supervisor.

6. OP did not scam or cheat the system. He just made poor choices. There is nothing legally or morally wrong with booking single tickets when they are cheaper. There is simply a greater risk involved and that risk is generally covered by allowing for a lengthy time at the intermediate airport. A <1 hour ground-time between 2 tickets will get you exactly what OP got (+ administrative fee for using Expedia). Only OP can value risk vs. reward overall. Do this 10x/year and save $350 each time, you are $3,500 to the good. Mess up once like this and you are still way up.