I'm in the, do what makes you happy camp. If there is one thing I've learned from competitive pinball is that no matter how much some people practice they will never be good enough to get past a certain point in a game. I feel fortunate enough that with enough effort I feel like I can beat any game out there but I also know a large % of players aren't that way. Which is a shame that some people wont ever get to have the fun of playing Megakrakolodonus Rex much less Clone or Final battle without making those changes. Before making a change to the number of balls, diffidently adjust the outlanes first and then maybe make the slings less sensitive. This can make a drastic difference in the difficulty of this game while still keeping the traditional feel of having 3 balls.
Last thing to think about. Before going in and setting the game to default at 5 balls, go into the settings and have replay award an extra ball. Then set multiple replay values. This can help you get through the game like you are wanting but also still challenge you do well while playing. For Deadpool, maybe have replay 1 at 750 million, then the next at 2 billion. This would make the game 5 balls but only if you were on a streak. Scores are under the assumption you wouldn't see them all the time. Adjust to your fitting.
At the end of the day, these adjustments are there by the game designers for a reason. They are there to help you make the game as much fun as possible for YOU. Just don't go posting high scores and bragging about them publicly without stipulating the changes that you made. That's really where you would get the most deliverables flack from the community is if you post a super high score but don't tell people you are running 10 balls, with no tilt, and closed outlanes.