Are the reflected and absorbed components of an antenna actually orthogonal?
You don't have the right picture of what's going on. Not least, that 0=integral equation. While it might be correct in a mathematical sense for some specific application, as Obi-Wan would say while waving his hand, 'this is not the application you are looking for'.

The reflected component can bear any phase relationship to the incident wave, depending on what is doing the reflection. A low resistive impedance and a high impedance will reflect in opposite senses, a capacitive or inductive reactance will reflect in quadrature to those, and in opposite senses to each other. When you have a reflection on the end of a significant path length, like the leg of a package, then it will rotate round all 360 degrees as move along the track.

The absorbed component is, by definition, in phase with the incident signal. 

If you choose to represent any signal as I and Q components, then they are in quadrature by definition, not because of any property of the signal, or circuit that it's passing through.

Forget breaking the signal down into components, and incorrect notions about the phase relationship between absorbed and reflected waves. Concentrate instead on the point by point impedance of the transmission line that passes from your active device, through the pad, bond wire if there is one, package lead, PCB pad, and into transmission line on the board. Although you sound like only the IC designer, you are also responsible for the IC to board interface (you can't use a chip you can't mount!) which includes the recommended footprint, and possibly the board thickness and material to ensure a good transition to the final transmission line on the board.

Analyse each part of that path in terms of length and impedance of transmission line, though the bond wire could be treated as lumped inductance, and the bonding pads as lumped C to ground, and then cascade those in a suitable RF simulator, and see what you get. 

Hint 1, the closer each part of it stays to the same impedance, the better.

Hint 2, you only have to worry about the relative phasing of reflected waves if your interface is electrically long, and different 'bad bits' are reflecting significant signal, and they are adding up badly as the frequency changes. Then you are really in trouble. Shorten your interface, or design the impedances better to reflect less.

Hint 3, absorbed signals are never seen again. A good interface should not have lots of loss, on inputs that creates noise, on outputs it robs you of output power. But it improves matching.