I am not sure if I got you right but for F# I would build up a major scale as you described (ton, tone, semitone,…) with the scale steps and then tune your oscillator to F# when the sequencer is at the playing the root note. It’s only about the relative pitches in a scale not the absolute pitch of the root note.
When you do so you will see that using scale steps greater then 8 semitones (from one step to the next as in: tone, tone, semitone, 8 semitones, 5 semitones, tone, tone, semitone,…) is pretty unusual for a scale since you would pretty fast sum through octaves. (just re-read your post and understood that you pretty much got that point so just see the 8 possible semitone steps as a surplus…)
As I understood the bottom row with the rate notes it is built for convenience when you want to use multiple scales that are related to each other but vary in the root note.
The scale mode is built with a maximum of flexibility in mind.