Reading the POH I found that the Rated Horsepower at 12000 Feet are higher compare to sea level. I have in the past studied the back pressure of the exhaust gasses but I cannot completely understand how it works.
Back pressure affects power because the more pressure opposes the exhaust, the more exhaust gas is left in the cylinder when the exhaust valve closes. This trapped exhaust gas, effectively inert for purposes of the engine cycle, limits the amount of intake charge that can be drawn from the manifold at a given manifold pressure.
The more intake charge you have, the more power you get (within limits), so the less unscavenged exhaust you have diluting the intake charge, the more power you can generate for a given manifold pressure.
This effect can be mitigated to some extent with valve overlap -- where the exhaust valve remains open for a short time after the intake valve opens; this allows the incoming intake charge to push some additional gas out through the exhaust valve -- providing there isn't too much "back pressure" on the exhaust side.
I’m not totally sure here, but a clue does come from the Systems Description in Section 7 of the Seneca II POH.
The induction manifold is equipped with a pressure relief valve to prevent overboosting by the turbos at low altitudes. There is also a bypass orifice which sets to a maximum of 40” MAP, full throttle, at 12,000 feet.
Another factor is that the Seneca II POH recommends a maximum throttle setting of 39” MAP for a sea level takeoff and cautions not to exceed 40” MAP during this process. This restriction is placed until clearing 12,000 feet pressure altitude. Apparently throttle setting of a maximum of 40” MAP are allowed at this point all the way to critical altitude.
Which would probably explain this power discrepancy.