I don't know what type of science diet you feed (basic puppy, lamb & rice, small bites, etc..) but most have corn as their first ingredient. It's not the best food thats for sure, but it's not the worst food either. Ideally you do not want corn in it at all, especially in the first 3-5 ingredients. A lot of Science Diet diet's have it as the 1st-3rd ingredient. Corn is just a filler, it is not really good for you let alone a dog. That may be one reason why your puppy has a lot of "waste" because that food contains a lot of waste.


As far as your concern I agree with you. I don't think it wil do any harm, but if it is working out great now why change it. The less time in a crate the better. If she is having accidents in her pen & not the crate then yes I'd put her in the crate. But otherwise I'd leave it be, not because it will harm her or anything like, just she will have more room & the such. Besides she's probably already adjusted to this routine you have now.
If you plan on always crating her, even when she's older & trust worthy in the house, then yes, maybe crate her in the mornings, say every other day or so so she will adjust to changes better. But If she will eventually become a full house dog I'd let here have as much room as she can handle without having accidents.