Ummmm.... How long has your friend been doing what he does? I don't mean to insult, but it sounds like he's pretty green when it comes to these cars. And changing those turbos isn't a job for an inexperienced tech or someone who isn't very thorough. Just my 2-cents from being a BMW tech for the last 10 years and doing quite a few N54 turbo jobs.
As far as the "break-in" period, the DME has no idea the engine has new turbos. It won't limit anything, nor will it limit boost before the 1st oil change. I might take it easy on them for a few heat-cycles, but that's about it.
As for what's going on with the boost thing......I'm guessing something wasn't put back together quite right. There are a TON on o-rings that should be replaced during the job (oil and coolant feed/return lines, charge pipe, etc.). It's possible that one got pinched, causing a small leak.
The new turbos come pre-adjusted, so there isn't anything the screw up there. One thing that I have seen -- on the V-band style clamps that hold the cat-pipes to the turbos: if they aren't clocked properly, the wastegate rod can hit and prevent the wastegate valve from closing all the way. Just a thought.
And yeah, the engine does lose some oil during the repair. The turbos, lines, etc. all hold oil that is lost during the job. Your friend should have checked the oil level when he got it running. The last one I did lost around 1 quart if I remember right. You could also have a leak from one of the 4 oil lines that go to the turbos. Hopefully not, though.