Wastegate won't really matter for breaking in a new engine since generally during break in you aren't revving the engine high and making much boost.
Not sure what the recommended break in procedure is for your new engine, but on my built SP63 engine, the first 500-1,000 miles had a recommended RPM limit of ~3500RPM. Which, when you aren't going WOT almost no boost will be made at that RPM.
So long as you aren't thrashing the engine right from the jump it shouldn't matter.