I don't think game shape and injuries are in the same category as enthusiasm or home field.
Enthusiasm is affected by league and cup, and yet those things are already separated from B3 because B3 minutes don't count. So not only are you right that enthusiasm should be locked for B3, it already fits with the way minutes are separately treated. Teams in different countries have entirely different situations, especially later in the season, and some will more easily be able to keep enthusiasm high.
For home advantage I think you make the case clearly. Being neutral, at the very least in the knockout stages, makes B3 fairer and less random.
On game shape and injuries, I think its more difficult to make a case for a change there. If injuries would be unfair in B3, they're unfair anywhere. We've all seen teams' playoffs ruined by an untimely injury. If it happens in B3, its only the same as that. Game shape is already the same for everyone. I don't see a case for a change there either.