Guys, I think you are assuming that in most cases, except for hot temps, you will get max take off torque with the separator in BYPASS. I would think this would be the exception rather than the rule especially when you consider the torque limiter or lack thereof.
As far as I know, unless things have changed, the 750XL does not have a TQ limiter. This means your meticulous engineer would have done ground runs and adjusted engine settings so that you can ram your power lever forward and not exceed the maximum TQ (or at least not by much) with the system in NORMAL. This means, with the disrupted airflow when the separator is in BYPASS (actually 'closing' a door in the 750XL), the TQ WILL drop and be less than what it just was with the system in NORMAL. It may not be a drop by much at SL on a cool day, but the effect would compound with increased altitude and temperature. By the way, speaking from experience, you can get the reduced take off TQ as a result of: separator in BYPASS, increased field elevation, or increased temperature and still not be ITT limited.
Two identical aircraft to be piloted identically line up. Both are set at max torque and max rpm for the take off. One is in bypass and the other is not. Both ITT's are within limits though the one in bypass is or will be at a higher ITT.
The bit you have missed is that, although both are at 'max torque' (power lever fully forward), there is a different number on each TQ display. The aircraft in BYPASS achieving the lower torque. Think of TQ as being like your manifold pressure power measurement on a piston and you can answer this question.
3% on 500 metres is 15 metres so not a whole lot to be bickering about...
would I be displaying gross negligence in deciding to omit the 3% from my take off calcs?
Braver than me...