We checked with Ford and while they have not released many details about the new engine, they did provide some explanation. The EcoBoost, like other recent DuraTec-badged Ford fours, shares a block design with Mazda's similar displacement units. In fact, the EcoBoost block is the same as the Mazda L3T used in the MazdaSpeed3. However, the entire top end of the engine has been redesigned. Like the V6 EcoBoost, the four uses a new direct injection system that is presumably less expensive, allowing Ford to use these engines much more widely than Mazda does.
The Mazda engine also
So the two engines are built on the same foundations, but they are not the same engine.
Update: I mis-read the spec table on the MS3 engine and it does indeed have variable valve timing. However, the Ford engine exclusively uses the cam torque actuated system introduced on the revised 3.0-liter V6 last year.
[Sources: Ford, Examiner.com]