You're still ignoring the value of whatever it is you're buying for $2k.
You're not getting those 2060 points for $60. You're getting 2,000 points for buying something that's worth $2,000 (hopefully!), and then you're paying a $60 fee for which you get nothing of value except the 60 points - essentially paying a dollar a point. That's a significantly worse deal than paying 3 cents a point.
Yes, it would be an even worse deal if you were to use a card that charged a fee but didn't give you points. That just makes the deal with the Amtrak card "less bad", but nowhere near "good".
Hello? If you DON'T USE the AGR CARD, you get ZERO points. ZERO POINTS! If you DO, you pay $60 more ($40 more but no 1% rebate on the aforementioned cashback card) but you get 2000 POINTS (or 2060 if they give you points on the fee).
So, YES, for the extra $60, you get 2000 POINTS. In BOTH CASES, you get $2000 worth of goods but by using a card that gets you points, you pay $60 but get 2000 POINTS instead of ZERO POINTS!
The ONLY question is how many points you end up with if the $60 you saved by not using the AGR card is used to buy points.