Yes it can be due to several things.It's not Nostromo then so best not described as such.
Duct length in itself will have zero influence on anything in the 7KHz - 12KHz band; nominal tuning is < 100Hz & any 1/2 wave modes should be heavily suppressed and far below that region; if you have problems it's from a different cause. Very large, shallow chamfers may reduce a small amount of edge diffraction at the lower end of that range but primary influence will likely be in the ~1KHz - 3KHz region. You don't specify how you're identifying these issues, but I suspect some methodological variation may be at work.
Re the box, 16mm MDF will have audible colourations from panel resonance unless heavily braced and / or strategically damped with bitumen a la BBC type designs (albeit is a bit thick for those). The foam appears to be the type I recommend not using for this construction. Forgive me, but I don't recall what the driving amplifier is, but if it is not a high output impedance SET, then you may also have a mismatch, as that box was designed for those conditions.
Right now I am listening to a KlassD amplifier with ICEpower output stage. 2x500w. Of course, it may have affected the sound in the wrong direction.
Do not know if it has high or low output impedance.
When I used my tube amplifier, I did not experience the same disturbance in the 7khz-12khz range.
Certainly affects the amplifier.
KlassD has more controlled bass and is completely balanced from the CD player to the speakers but not as good treble.