That's a lot of words to say, "you're trading it in wrong."
Apple's trade-in values have never been reasonable IMO. Neither have the prices they charge for refurbished products.
From the article: "Apple is facing criticism online for offering poor Mac trade-in values following this week's launch of new MacBook Pro and Mac mini models."
Maybe that is poorly worded, but what was the trade-in value for that $50K Mac Pro BEFORE this week's launch of the new MacBook Pro and Mac Mini models? Was it just as bad?
So don't use it, Apple doesn't have a monopoly on 2nd hand Apple products. I look at it this way, for as long as I can remember the recommendation in the Mac community was that you never get Ram from Apple because the markup was too much. It's a little different now with Apple Silicon but I would say that for the Mac Pro specifically, you would have to be either silly or not want to go to the effort of finding third-party ram to max out a Mac Pro from Apple.
Who cares what Apple is offering, you don't have to take it and you shouldn't even consider it an option. This service doesn't feel like a way to save money on a Mac, no matter what the advertisements may say. It seems more like a way of getting more Apple products recycled.
Also, remember this, the $50k Mac Pro is $50k because of its upgrades, the machine itself starts at $6k, and a few hundred more for rack mount. Yes, you are trading it wrong.