[Angel And The Wolf]

The purpose of the Atkinson cycle is to allow more travel on the power stroke(30% more in the Prius engine) to extract more of the energy from the burning expanding gasses, and the same 30% more travel to push the (now lower pressure) exhaust gasses out.
The late closing intake valve looses that extra 30 % of air, before compression begins, so in the 1.8L Prius engine, effective engine size is reduced to a 1.4L engine for compression purposes, with an extra .4 ltrs of travel for expansion and exhaust.
This captures more of the power, and eases the energy needed to exhaust the spent fuel.

Closing your intake valve early would create a lower pressure in your cylinder which your piston would have to fight against in order to continue to descend.

Your best bet would be to regrind your intake cam for a longer duration open time, (starting at the same degree, but remaining open more degrees after BDC) realizing that whatever portion of the former compression stroke your intake valve remains open would reduce your effective engine size and power, while also decreasing it's pumping losses.

Don't forget to reprogram your fuel injectors for less fuel per stroke, and to not spray during the open intake valve period.

If you are worried about losing power for passing, you can install an electrically driven supercharger coupled to a Wide Open Throttle (WOT) switch for when you want acceleration rather than economy.