It used to be quite common to use a special bracket to piggyback the hard drive on top of the second floppy. The bracket moved the hard drive further back inside the computer case than it would sit if it was mounted in place of the top floppy drive.

I'm not aware of any problems - it was a popular setup. I had an SE FDHD configured this way for a number of years. The only downside I ever came across was that the proximity of the hard drive to the neck of the CRT sometimes resulted in very slight movement of the image in one corner of the screen when the hard drive was performing seek operations.