Yes, there are. To me it doesn't look like that the creation tools are stripping unneeded whitespace characters, but rather like either they are converting line breaks to whitespaces (would seem odd to me, if they would do that) or the script used for exploding to html misinterprets line breaks as whitespaces (that's only a guess of course).
Here's a small sample output from mobi2oeb from a selfmade mobi file. Notice that whereever there is "> <" there should have been a line break between:
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<guide></guide></head><body><br/><br/> <h1 align="center"><b>Book Title</b></h1> <br/> <h2 align="center">Author Name</h2> </body></html>