I probably don't have the patience to do lots of mathematics, but I find it hard to believe that there is any benefit in chasing IB+ status from IB flights - unless you fly often on very expensive flights or have little interest in the Avios to be earned.

Otherwise, those IB flights will still credit quite nicely to BAEC, Alaska or AAdvantage based on distance + multipliers + higher elite bonuses.

As for the Elite Point calculator, it probably just can't handle connecting flights and must be used flight-by-flight. No reason for the flights not to earn Elite Points as normal.