You could create a custom palette ID specific for the custom jobs, which would work only for that custom job .
And I understand your view. RO standard palette would be considered a palette full of errors in our current days. However, it's design, even if it's not that good from an artistic point of view, it's very good for game graphics production and recolor-making. It's main advantage (regarding production) and main disadvantage (regarding artistic color quality) is the fact that color ramps are separated, and somewhat individualized.
If we see top-notch renowned pixel artist, they create palettes like this:
(By pixel artist Adarias)
Which are definitely better than any palette with a similar organization like RO (separated color ramps).
This, however, doesn't apply to RO, since we are looking to make graphics production and flexibility (ie, creating recolors) faster and better.
However, I believe we could get both advantages, fast production and flexibility with good artistic quality, if RO palette was somewhat like this:
(Art and palette made by Japanese pixel artist Syosa, one of my favs)
I'm wondering now if this could be also tried with RO palette (like making all 8th tones in all ramps the same color = blueish dark pink). Maybe Kamishi surprises us xD!