Estimating for Ipe stairs: How do you handle the labor markup?

I am currently bidding a custom staircase job using 5/4x6 Ipe with double-return nosing, and I am curious how you guys are handling the labor markup on these complex builds. On standard deck framing, I usually charge per square foot, but these stairs are a different beast entirely. Between the meticulous template work for the landings and the sheer amount of time spent pre-drilling and countersinking every single step to avoid blowouts, I feel like I am constantly underselling the man-hours. For a typical set of 15 hardwood stairs, are you guys billing by the flight, or strictly hourly? I have been quoted around $250 per step just for the install, but that feels low considering the specialized blade wear and the time spent oiling cut ends with AnchorSeal. Any advice on how you structure these quotes to protect your margins?