This is precisely why I train bare knuckle and encourage my students to learn how to strike bare knuckle. Getting used to striking the bag, or other students, with gloves on encourages poor weapon structure by removing the immediate results of it. If you don't have to focus on hitting with the proper part of the weapon, any weapon, then over time you lose that focus. I would only advocate the use of gloves when doing very intense drills with heavy contact, and even then I would encourage students to progress beyond the need for them.
At a beginner level, yes, I glove my students for sparring. But over time, I expect them to develop the ability to strike safely and accurately without the need for gloves. And we train that way.
If you are training for a fight where you will be wrapped and gloved, then train that way. If you are training for a fight where you will have a gun or knife, then train that way.
If you are training for a fight where you will be both empty and bare handed, then I think you should train that way.
-Rob