Back squats, behind-the-neck work and heavy carries are what an irritated neck usually objects to. Front squats with a cross-grip, neutral-handle pulldowns and chest-supported rows are the usual substitutions people make.
The honest limitation: RepRoute's exercise catalogue carries joint-safety data for 7 regions only — shoulder, elbow, hip, lower back, knee, ankle and wrist. Neck isn't one of them. Flagging it records the injury on your profile and changes nothing in your generated plan.
Tagging the catalogue for the neck by guesswork would be worse than the gap it fills — a wrong safety tag is a wrong exercise put in front of an injured person. Until that data exists and has been checked properly, we say so plainly.
The manual route works well here. Flag the neck so it's on file, then use Swap during your session on any movement that loads it — a bar on your back, a heavy carry. Swap hands you another exercise in the same pattern that fits your equipment, one tap at a time.