I might re-check the crank bolts once after you start riding, but not repeatedly.
If the face of the crank is curved, then a portion of the extractor might stick out.
However, your crank appears to have a face that is flat (perpendicular to the bottom bracket spindle. So, I'd expect the extractor to be flush.
If that crank face is actually perpendicular to the bottom bracket, then that extractor is not normal, and trying to use it could cause binding and/or stripping of the threads. I'm surprised the threads are "OK" as it looks cross-threaded.
I'd talk to your manufacturer, especially as that looks like a very expensive crankset.