Larger 'innovative' projects ostensibly run by young researchers are often projects the institute/professor had already planned and done some (mental/political) groundwork for, rarely (ie never) were they on the intiative of the young researcher. Bandwidth for personal input from the young researcher was in practice very limited. Might have been a peculiarity of the department, afaik they attracted very few with their own money (and thus their own direction).

The further you are from the clinic and thus the bread and butter of the massively overpriced commercial instrumentation makers, the more freedom there is. So, whatever you choose, your impact is limited. If you want to make a real difference, my impression was that you better cozy up to industry or step over altogether.