First, a little terminology:
Scales are groupings of notes which span an octave (IE from C to the next C, in any key.) Scales exist regardless of instrument.
For reference, a KEY is not a scale, but follows the order of natural major/minor (IE CDEFGABC), can be spelled out using all 7 letters, and uses either sharps or flats but not both. This is basically the keys that could be written on a music staff. For this purpose, key is defined by having 0 to 7 sharps or flats, with the remainder being natural. That means you can have weird stuff like C# or Cb which have 7 sharps/flats, and sound the same as other scales (IE Db) even though they read differently on the staff.
Systems like CAGED are concepts for navigating the fretboard, so they are instrument-specific approaches, not instrument-independent scales. The way you finger notes for a given scale on a guitar would be completely different on a cello, piano, or saxophone even if you are producing the same pitches.
The goal of all these systems is ultimately to do a few things:
Understand your fretboard
Locate appropriate notes quickly
Play with efficient fingering patterns and minimal shifting
Provide you with the physical tools to locate and play musical ideas, which are going to come from you, not the system.
Every great bass player, I'd say even every good bass player, knows their fretboard well. You should be able to hear any note named and locate it in multiple positions immediately. The next step is understanding intervals, because as bass players much of what we do is based on spelling out chords or melodic elements one note at a time. If someone calls out C you should know that G is the 5th and that there's a G on the same fret, one string below your C, or above your C by moving up two frets and one string.
Every interval connects to the tonic (root) with patterns that, on the bass, are easy to move around and never deviate unless you get into odd tunings. So, knowing all your intervals, and all your note names, opens up the entire fretboard.
Scales are just groupings of those intervals, packaging them together. Your church modes (the 7 modes of the major scale) are usually a good starting point because that's the foundation for all Western music. If you master those you can play pretty much anything, and all the things that are NOT within that system, like harmonic minor, melodic minor, whole tone, diminished, etc. are all much easier to understand because they are taking this thing you know really well and just making small adjustments. If you can rock your Aeolian (natural minor) scale really well and blaze it up and down your instrument fluently, then it's a lot easier to master Harmonic Minor, because it's the same thing with a natural 7th. You aren't really learning a "new" scale as much as adapting the ones you have already mastered with some new shapes.