This might be a biased opinion, because it's how I do it and it works for me (ymmv), but I think starting with for example the major scale patterns in 3NPS is a great foundation. Once you know this by heart, and especially have learned the relative degrees of all the frets in the pattern, it becomes easier to learn a different scale formula relative to this major scale.
For example, when learning the myxolidian mode, I might go: "oh, but that's just the major scale with a lowered 7th degree!" And then I can apply that pattern easily on the fretboard.
Now, as for why this tool is useful (to me at least): it's really quick to visualise a position in a certain scale in a certain key, and show the note degrees (it's the "roman notation" setting). Especially for really exotic scales that have a lot of differences to the major scale (e.g. messiaen's modes), it is very useful to have a visual aid in front of me while playing.
i've been teaching myself the guitar for a couple of years and I'm wondering how to use this tool: for what use cases do you refer to a scale chart?
Till now, i have committed a few scale patterns to memory and i derive the rest when i want to improvise