Some master cylinders come with a removable plug in that hole. Do you see something in there that might come out? If yes, get that plug out of there and your long rod might work fine. Sometimes a royal pain to get out cuz they fit tight with o-rings and there's nothing to grab. I've carefully glued the head of a roofing nail to a plug with JB weld in the past and let it cure overnight, so I'd have a nail to grab to pull it ou of there. Worked real nice.
But if there is no removable plug in the MC, then I feel you might as well just cut/grind the long one down that you already have. A brand new rod is no guarantee of proper length, even if it seems like it fits when you install it. A few trial and error cuts of your original and you'll find the right length, then fine tune with grinder and several more trial and error fits.
Even the brand new rod that came with my all-in-one booster/mc kit from getdiscbrakes.com needed a touch of grinding to get appropriate pedal free play. A rod that is just 0.5 mm too long will start to gradually apply your brakes due to underhood heat buildup & metal expansion, and cause all kinds of problems...all the way from a loss of fuel mileage, to destroyed rotors and pads, to possible complete loss of brakes due to boiling fluid.
Just make darn sure whatever rod goes in there provides proper pedal freeplay.