Homemade rules are like cooking meth: your end product can have high pay off (especially if you pull it off masterfully), but you run the risk of the whole experiment blowing up in your face. It's no mystery among the players in my games that I'm fond of bending some rules in any tabletop platform; and I can argue that published books often remedy their own past rulings because, well, they don't always gel with the game. Simply put, some rules are meant to be broken.
When I studied American Folklore in college, I did an anthropological study, well, more of a collection, around the American house rules found in Monopoly. My main method for the collection was interviewing and observing game play. I was pleasantly surprised when I found out rules existed that in 20-something years of living and playing the game, I had never even heard of. Take this one for example: when you own more than one rail road, you may warp from one track to the other, if you happen to land on one of them. Further, you could charge players any fee you wanted to allow them to warp on through, if they happen to land on one as well. Fascinating concept. Want to avoid a string of high-priced, renovated neighborhoods? No problem.
Then there are some rules of Monopoly so famous, they are commonly thought of to be the actual rules. Take the "Free Parking" space, for instance. Ask yourself, what does the space do? What are the rules around it? If you answered anything other than "nothing at all", then you have played the game incorrectly long enough to believe the space has a purpose; or, as I argue in this post, you have chosen to adopt a make-shift ruling absolute, because it is better than what originally existed.
A DM has the opportunity, when it comes to the rules of the game, to make some stuff up. If it is intentional, and it works, why not? I've known some DM's to change whole feats, integrating them into others, because let's face it, no one wants to waste a whole feat on some the lame options that start some really attractive feat-chains. DM's who carries over made-up rulings across games and throughout different player groups has a unique opportunity, perhaps, to build something of a legacy for themselves.
I do, however, think DM's have a responsibility to inform players that some rules are made-up. As a player who for certain thought "retreating from battle" allowed me not to provoke an attack of opportunity, boy did I feel stupid when I brought this rule into a game of experienced players.
When it comes to rulings, it should be a simple, mathematically-moral equation: breaking the rules can be bad, making the rules can be good. Create something unique that many players love, and you have something of a Dm'ing legacy; do the opposite, and go down in infamy.