the 98-99 srx uses the fatter or bigger main jet on the mag side cylinder. The 2000-02 uses the larger jet on the pto cylinder. The ignition system is the reason the 98-99 uses the jetting this way the mag cylinder is closest to the stator and the all 3 cylinders spark at 1 time.
The 2000-02 uses a 3d ignition system and only fires the spark plug for the firing cylinder and not wasting the spark like the previous system did.
what your describing is staggered jetting, nothing wrong in doing that its just its really not needed unless the engine is modded and say the set of aftermarket pipes is designed to run over top of say the mag cylinder, that cylinder might require slightly more jet due to the added heat of the pipe being over it, lots of examples of what you can do to jet.Youll find in a stock setting or with factory pipes it wont be needed.