I'm certainly no structural engineer, but ...A number of people here seem to be assuming that a joist larger than the minimum can have holes drilled or notches cut in it and only their incursion into the minimum "zone" taken to be of structural significance. ... I am not a structural engineer, and I suspect neither are they, but I very much doubt that they are right.
...consider a joist which is of just the minimum permitted dimensions for the application/span, with a hole of permitted size drilled at its vertical mid-point (at a point in a span where drilling is permitted). This is compliant. Now imagine 'perfectly bonding' a substantial additional piece of timber to the top of the joist. The drilled hole is now considerably below the midpoint of the joist (hence maybe not compliant) - but is it conceivable that addition of that extra timber has actually made the joist structurally weaker? That appears to have been the basis of the OP's point - and my non-expert intuition finds it hard not to sympathsise (unless/until I am otherwise educated!).
Kind Regards, John