I think it may be less confusing if we back up and start from square one. You mentioned that you are working on a "project breed", what is the project? Can you post pictures of the rooster and the hen with descriptions of the breed and color you believe each to be?
In the first post you mentioned that this is a project breed. In a project it's not unusual for unexpected recessive traits to pop up. "Purebred" doesn't mean much in chickens since breeders rarely keep pedigrees and what matters is that the resulting birds have the same appearance and can pass those appearances down to their offspring consistently.
As an example, orpingtons come in a lot of colors, but the very first variety (black) and the current most common variety (buff) come from completely
completely different breed crosses. Black orpingtons were created using minorca, plymouth rocks, and langshans. Buff orpingtons were created using gold spangled hamburghs, cochins, and dorkings. Both varieties are judged using the same standard with the exception of color.
These days it's more common to create new color varieties by crossing a breed that already has that color into an established breed, but that hasn't and isn't always the case. Either way, that's how you can get things like incorrect comb type, incorrect body type, wrong number of toes, etc popping up in project birds.
it might help to consider that you are working with three different factors in project birds. Breed type (comb type, body type, number of toes, feather type) Color (black, blue, white, red) and Pattern (solid, partridge, mottled, laced/penciled, duckwing, barred, etc). These factors are not necessarily connected to each other and can be considered independently.
(Sorry if this doesn't make sense, I rambled a bit there especially with the orpington facts but I wanted to point out how there's more than one way to create a variety that fits the breed standard and how little "purity" matters for chicken breeds)