I'm not sure if I understand why measuring vertically and horizontally to a point on the saddle is any more difficult than measuring frame stack and reach? Why don't you use measure an angle and length to define the location of the top of the head tube? Measuring seat location "X-Y" should be just as easy as measuring head tube top location "X-Y". Besides, I don't see an angle measurement in this figure:
I'm looking at it from the standpoint of consistency in measurement. Yes, the saddle to pad location is important, BUT those can be either inputs or outputs. You can either measure them directly off of the bike in "X-Y" and then calculate the cockpit length and drop from those measurement...OR, you can do it like you prefer and then calculate the "X-Y". At some point those locations need to be translated into the "X-Y" coordinates in order to use them. My preference, and I'm coming at this from someone who deals with dimensioning and tolerancing on a daily basis, is to take the measurements directly from the chosen datum. That reduces errors in "setup to setup".
The dimensions you show can still be calculated and displayed as "reference dimensions", and would be the "quick and dirty" dimensions you could check to make sure things are where you think they are.
BTW, I have an idea for a fit bike attachment you could have made which would basically create a "fit bar", in other words, the aerobar version of a "fit bike". You could have made a device which allows you to position the pad locations and shifter locations in the X, Y, and Z coordinates (relative to the headtube top) and then you can directly read those coordinates off of the device and add them directly to the stack and reach coordinates read off of the fit bike. That way, you wouldn't need to actually stock a sample of each bar and stem type. You can merely have measured them once and then set up the "fit bar" to each candidate bar's particular coordinates (including the adjustment ranges). Same thing with particular combinations of stem lengths and angles, along with any spacers or head caps. You could fit someone on one of these fit bikes and be able to specify a complete bike/stem/bar/saddle setup without ever actually mounting any of them on the particular bike. What do you think?
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