Hard to say what the effects will be without knowing the details of the head.

It's possible that the shorter valves are mated to larger shims or higher lift camshafts or something...

If it's the later model, the shorter valves are probably for durability at higher rpms versus the older valves... But if the newer head has more recessed valve seats, perhaps the head and valves will yield lower compression that will also allow more boost.

Unless you have access to data on compression ratio differences between the two versions of the 4D56, as well as data on their rev limits, you can't say for sure.