"Should the avr or inuke handle lpf ? Is there any difference ?"
great question. might want to add it to the faq.
most avr's place a 4th order lowpass (24db/oct) filter on the sub at the crossover frequency**.
jointly, they place a 2nd order electronic high pass on the mains, which taken together with the (assumed) natural/acoustic 2nd order (12db/oct) rolloff of the mains (which frequently isn't even the case), combines to create a NET 4th order 24db/oct high pass.
since the NET slope of the crossovers between the main and the sub are the same, phase rolls over 360 degrees, but the drivers are in phase at all frequencies.
if someone were to slap an additional 2nd or 4th order electronic low pass in the inuke, then phase would rollover 540-720 degrees, but importantly, it would NO LONGER BE A MATCH AT ALL FREQUENCIES, so some frequencies would be in phase and other would be out of phase with the result being unpredictable cancellations at various points in the frequency response.
best to leave the low pass filter on the inuke OFF and let the AVR handle those duties.
**here, by crossover frequency, it is meant something like 80hz. this is completely separate from the protective high pass filter on the sub which would typically be around 15-20hz or so and that one should be run in the amp/inuke/dsp.