There isn't a single thing....
wrong with leaving extra steerer tube on the fork. I and thousands of others have been doing it for years! I usually leave between 25 to 30mm extra to begin with to facilitate changing stem positions and fine tuning the fit and riding position. Once I've got it dialed I may cut it down a bit. Just depends on where the stem ends up. I usually try to keep it down to no more than 25mm above the stem. If I really like the bike and fork combination and don't plan on selling the fork before it dies then I'll do a permanent cut.
I've NEVER made contact with the steerer tube with my knee(s), hit it during and endo, or anyother crash that's happened. I could see the concern if you were leaving more than an inch or so of steerer on the fork and it extended above the level of your bar. But an inch to an inch and a quarter won't hurt a thing.
Go ahead if you wan't to. It gives you a wider range of fit adjustment, and it can help in making the fork more saleable (not increased resale value) as the longer steerer tube will allow it to fit a wider range of frame sizes. The more frames the fork will fit the better the chances that you can sell it.
Your, choice.
Good Dirt