[jeroengeerinck]

So thanks for thinking along.
I have found a solution. (? the solution)

Protools HD has this option that says 'compensate for input delays after record pass'.
It is located on the 'input' tab off the I/O window.
This nicely aligns sounds from both interfaces and solves the problem.
Well it makes it possible to the interfaces together, but the issue off course remains that whilst sound checking it'd still be hard to sort out phase problems, by hearing since the alignment can only happen after the record pass, which is off course logic.

Guess I'll need an avid I/O with the same architecture inside as the omni, then this small shift won't happen I presume.
But first I need to get my hands on an HDX + a new PT12HD license.