I agree that Atkins sold low in almost every situation, it is one of my major gripes with him, but that goes back to my earlier point. They spent 1.5 years pretending to contend. They never made a real attempt at going for it, nor did they trade anyone at peak value. They rebuilt in the background. That's why the farm is so good primarily due to drafting and international signings. They didn't trade prospects for big league help, they plastered the team with cheap vet plug ins they signed for little in free agency. They didn't trade vets at peak value, they held on to them to try to stumble into a WC spot hoping the weak AL stayed weak (then the Yankees got good overnight, and the rest is history). It was the most risk averse and hedge conscious a team could possibly be, likely do to ownership seeing $$$$ and not wanting to derail that money stream before they had to.
Rebuilding teams are not all built the same. Some teams make great trades. The Jays don't. Some teams draft and sign international talent at a high level. That's where the Jays are. My point and your point are the same I think, the team would be in a much better spot if Atkins was a better trader combined with the drafting. Unfortunately he isn't, but luckily he hasn't been stupid in areas besides trading, so it mitigated a lot of the damage. The Jays are in a decent spot because of it.
The one thing that hurt the Jays is that once they embraced rebuilding, it was too late to not only get value for their existing vets, but also get value in the trade market period. For some reason, maybe it was the CBA agreement shortly before the 2017 season, teams began to value prospects differently than they did previously. You can't trade for top prospects anymore. I don't think Atkins is clever enough to fleece a GM anyway, but having vets to trade nowadays is almost a disadvantage unless they come with many years of affordable control.