There exist rules about decorations on robots (<R8>), but no rules I can find on "decorating" field elements. The closest rules I could find are <T11>, which relates specifically to repairs.
The manual authors appear to be aware of the potential referee-ing challenges associated with <SC5> sections (c) and (d). The manual makes specific note of cases where "a referee is uncertain."
In both (c) and (d) cases, referees have to be able to distinguish between two identical balls that are in motion simultaneously, in addition to dealing with their other duties.
To assist refereees with tracking balls, would it be OK for EPs and other field element providers to "decorate" the balls in a manner to permit easier in-match identification? For example, a permanent marker to draw different shapes or numbers on each ball in a match or set of matches (assuming balls will get mixed up). This way a referee can short-term memory recall quickly that "ball #2" or "the one with the red triangle" was the Rapid Loaded ball, and has recorded a Pass already.
One potential concern I can see is if there are teams hoping to use sensors to find balls based on color. In this case, guidelines may be needed on the extent to which a Ball may be modified, and/or a warning for programmers that events may have variations on the Ball colors and patterns. BTW, for autonomous, or Skills in general, EPs could just provide unmarked Balls - if this is an issue. Those kinds of matches don't need referees to track Passes.
I'm sure the GDC has done a lot of match testing, probably discussed this already, and perhaps there are reasons for not being too concerned about the need to mark Balls? If it's not OK to "mark" balls, then please make that clear as well. Although, one could "get around" this perhaps by "repairing" balls with different colored thread, or even use different colored hexagonal or pentagonal repair patches as permitted by <T11>.