I look at in place/parallel decision on a case by case basis. If the install is going to take days/weeks to do, then parallel. If it is going to be something accomplished in a half a day or less, then I'll do and in place after making a backup of the entire MAS folder. I still encounter issues with the parallel install (e.g. custom office panels, etc). Plus I still store most of the paperless files under the MAS_XXX\paperless folder, so resetting the indices are a PITA. I have started setting the paperless folder to a location that would not change when doing a parallel, but this is a minority of installs.
I think Sage got it right on being flexible in v4.5.