I don't know that it's a totally different department. Engineering is a highly-compartmentalized field. People aren't generally transferrable between groups such as chassis engineering and drivetrain engineering, for example. My guess is that the same engineers who worked on the Air chassis tuning -- David Lickfold, for example -- are the ones doing the work on the Sapphire suspension, as their work on the original Air is mostly done.
It's important to understand that almost all the differences between the Sapphire and other Air models are in components that are already nailed down for the other Air models. Thus applying engineering effort to the Sapphire's brakes, suspension, chassis tuning, aerodynamics, front seat design, etc. is more likely to impact development times on models still in development (such as the Gravity SUV) than production times on the Airs.
I guess one could argue it increases sourcing and assembly complexity, but I think those impacts would be minimal. If it becomes difficult to get the unique Sapphire components from vendors, then very few cars (the Sapphires only) will be affected. As for the assembly line, I don't know that it makes any difference to an assembler whether he's installing a Sapphire sport seat or a Santa Monica or a Tahoe or a Santa Cruz seat in a standard Air, or whether he's mounting a Sapphire wheel or any of the several other Air wheel options. Most automotive production planning systems are designed to handle an array of option installations on the same line.
The biggest impact on production planning might actually be the blue paint, which will either require a separate paint line or the switchover of an existing paint line. But they probably do switchovers to batch the colors, anyway, and can run the panels for the whole Sapphire allotment in one batch.