The closed deck shortblock configuration isn't much of a benefit until you hit seriously high power levels. Even the open deck subaru blocks will support 500+whp before they run into problems with cylinder wall deformation/deflection. If it's an NA motor I'd definitely want open deck or semi-closed deck for weight reduction. An NA 2.0 will have a hard time generating enough cylinder pressure to deflect the cylinder wall enough to matter.
The engine you're describing above sounds like a pretty good description of an EJ207 with direct injection, instead of a turbo
Equal length headers really would be a good improvement, so I definitely agree with that.