The basic idea is this: all players are ranked based on the annual average value of their contracts, including LTBE incentives and NLTBE incentives earned in the first year. The highest player receives a point total equal to the number of players with contracts (this year, 2164). The second highest player receives one less point (2163), the third highest player gets one less, and so on down to the lowest-paid players.
Then, there are a couple of adjustments. The main one is playing time: players who play 25% or more of snaps on O or D get a point for each percent. [There's a different system for K and P.] Also, there's a 20 point bonus for being named All-Pro.
These sums are added up, and then percentiles determined. Comp picks are based on those percentiles: >95th = 3rd, >90th = 4th, >85th = 5th, >75th = 6th, >65th = 7th. Brady, for example, ended up around the 99th percentile, so he earned a 3. Van Noy and Collins were both in the low 90s, so they were worth 4s.
The only explanation for what happened here is that Damiere Byrd ranked around the 63rd percentile before accounting for play time, but played almost 90% of snaps. That gave him a bonus 90 points. That must have moved him above the 65th percentile, while Elandon Roberts (40% of D snaps) and Nate Ebner (ST only) fell below the threshold.
The rule for canceling out picks is that you cancel out within the same round first, then lower rounds, and then higher rounds. Phillips and Allen canceled out Shelton and Karras (all 6th rounders), meaning Byrd canceled out Collins. :-(