I'll jump in here - I think if you hear something you like, you have to study and learn to applyl what's happening in your own way. Maybe you've been doing this.
i listened to some of the tracks and even put the rudimentary peni album into Moises so i can turn change the mix around to hear what the bass was doing in relation to other instruments. What i hear starts with playing roots - fine, but then there's walking to connect to the next chord - sometimes its a 1-3-4-b5-5 kind of thing. Somtimes it's pentatonic, sometimes it's playing around with octaves or approach tones. All this to say i'd start with what is the root movement. Play only roots for awhile - get it in your ear. Then you can add things - approach tones (a step or 1/2 step above or below the next note), or add other chord tones - 5ths even. Or add scale walks up or down to the next chord - use your ear to determine the quality of the scale (minor.major, pentatonic). Sometimes the vocal melody might matter. So to approach a song:
1. what's the basic chords and root movement - i get the sense your question is beyond this - how to create interesting lines over those chord changes.
2. For each chord what are the chord tones and more importantly how do you connect this chord to the next one?
2a. sometimes the melody can provide clues so it's always good to play the melody or at least hear it as you connect the bass to it
Yes it's theory but it's pretty basic. That said, this music is not easy - some of the chord progressions are angular and the tempos are wicked lol. The concepts of what's happening to create melodic bass lines are not that complicated though. You can learn them on simpler things and then apply it here. it's the work of a lifetime. it will take time and many small steps.
An example of an amazing line in another genre is James Jamersons Darling Dear. Lots of chord tones with chromatic approach. Note how the bass meets up with the vocals here and there, like where the vocal says "to be sincere, and true love will appear.." at about 1:40. A lot of what's happening here is also happening in Rudimentary Peni believe it or not.
Thank you for the in-depth reply!
I try to think in terms of chords with the bass too indeed. I think that, as you suggested, it might be a good idea to try playing over a guitar track in real time rather than think it theoretically by just watching a tab and playing the bass alone...