Imo, learning bass lines note for note is good training.
Absolutely: there IS a point to learning bass lines note for note, even if your goal is not to play them that way. The ability to learn by ear is an
incredibly valuable skill. Practice, practice, practice. Eventually you will get to the point where you can learn simple bass lines just by listening to them, no need to parse them out on your bass. Keep practicing, and you'll figure out intermediate songs by ear... you get the idea. I don't claim to have the greatest ear, I rarely play jazz or progressive tunes, but I can usually figure out the bass lines of the cover tunes played by my bar bands just by listening to them: I'm talkin' rock, pop, r&b, blues, funk, country standards. I don't miss the days where I had to hunt and peck to figure out bass lines. Even with trickier bass lines (Rush, Chili Peppers, etc), I'll have a good idea just by listening, even if I have to sort out the details later.
To learn by ear, it helps to know basic chords and scales, starting with major and minor. Dorian and mixolydian scales are also helpful, as are the pentatonic/blues scales, and basic blues walking. Get that basic training if you can, for starters.
In Crossroads, Jack mostly sticks to minor pentatonic scales (A, E, D), but there are plenty of exceptions such as chromatic blues walking, some cool F#s (A dorian mode), etc. The "mystery note" in question is definitely a G, as noted by others.
I don't believe anyone would argue that the Cream's Crossroads must always be played with Jack's bass line, however Jack created some really nice hooks that some non-musicians recognize and it's good to know 'em, and throw 'em in even if you're mostly doing your own thing.