i. e., the figure is presented in universe as having yellow skin alongside other figures with realistic skin.

While there are no other minifigs in set 10687 with human skin exposed, the Scorpion figure in the only other Juniors Spider-Man set (10754) has Light Nougat printing that shows his face. All other licensed Juniors figs also have realistic human skin tones, if applicable. This would suggest that the Spider-Man subtheme and licensed Juniors sets overall are supposed to have realistic skin tones.

Exclusions for yellow skin tone where there otherwise would be realistic skin tone:

• Cases such as Harry Potter and Star Wars minifigures prior to the standard of realistic skin tones for licensed characters
• The 20th Anniversary Star Wars figs and sw0985 since those are presented outside of the context of the other Star Wars figures
• sw0122 is iffy, but ultimately it lacks a face for the head to actually be skin

The closest instance that I can think of is some figures from The Lego Movies or Lego Dimensions, but that can be excused by the characters being from different universes. Although not representing a human, the minifigure bob015 has yellow hands in contrast to its lime green fish headpiece, likely due to budgetary reasons in manufacturing.

Edit: The new closest case is the figure min077. This is also a bit iffy since it’s not clear if this figure overall is a costume or if the yellow printing represents the actual flesh of the character.