Comparing apples vs. oranges is tricky, but we can account for certain factors (differences) that have known quantitative effects.
A few things to keep in mind here:
1) Chris Johnson's 100m times are from high school, and shouldn't be the [unadjusted] gauge for comparison to Bolt (or other T&Fers). I guarantee CJ can run faster now than he did in HS.
2) Within the course of Bolt's 100m races, using the timed 10m splits, Bolt's best time over 40yards was approximately 4.39 (some have suggested 4.37). This is actually similar to the 40y split for Maurice Greene's 60m WR.
Of course, Bolt's strength is in the latter part of the race: 40m to 70m or 80m, where his top end speed pulls away from the others.
3) HAND-TIMED START: CJ's famous 40y time (4.24) at the NFL combine was achieved using electronic timing, but that is only at the finish. The start is still hand-timed, and with the most skilled human timers who are practiced at this, there is a reaction time of approx .10 to .15 after the runner has started. (The timer reacts to the runner, not vice versa as in track.) To equate the NFL 40 to a track time, we'd need to add .10+ here to CJ's 4.24, giving him (generously) a 4.34.
4) REACTION TIME TO GUN: For top 100m sprinters, these range from about .15 to .22, with Bolt's WR sprint having a reaction time of .165. If you had CJ's 40y time in reaction to a starter's gun on the track, add .15+, giving him about 4.39. (again, generously)
Note that these adjustments, correcting for timing procedural differences, have Bolt & CJ at almost the same time for 40 yards.
5) STARTING BLOCKS: Track uses them; the NFL Combine's 40y doesn't. The starting blocks help HUGELY to those who have trained for track to take advantage of them. How much (in seconds) do they assist? I don't have any data on that..... and won't venture a guess. But given that we have CJ & Bolt equal in the 40y with the other adjustments with Bolt using blocks and CJ not, I'd have to presume that if both used blocks, CJ would definitely beat Bolt in the 40 yards.
But as any of us who have watched Bolt run 100m, 150m, 200m knows, many folks are close to (or occasionally ahead of) Bolt at 40 yards. And then... then he is gone.
I'd bet at 50meters, we'd have a very close race. Over 100m, my money is on Bolt, but I do believe CJ is running 9.90 to 9.95 range. And I wouldn't be surprised to see CJ crack <9.90 on the lucky day when his RT is dead on.
And btw: even if CJ has the NFL's fastest 40y time, that may not necessarily mean he's the fastest NFL guy over 100m. I'd bet there are a dozen guys in the NFL who could break <10.0 for 100m, but the bigger money & bigger fame is in football, not track, so they end up going that direction.