It is not, however, at this time supported by UltraCompare Lite or Professional, nor any other product that I am aware of.
Since "white space" (tabs and spaces) can be ignored completely and discarded, it is "technically" true that line terminators could be "discarded" while comparing, however, since the compare utilities have to show you the "line by line" differences, it would be impossible to visually show you where the differences are in the files. The utility would be limited to stating "files match" or "files do not match." Not very helpful. I suppose someone could come up with a way to visually "compare" the two uneven lined files, however, it would not be easily understood by the average user, and, quite possibly impossible to understand for most. It would, at the very least, be a very ugly representation.
What you really need is a code formatter to reformat the code in a more readable format before you do the compare. Running HTML Tidy on an HTML document will fix those lines up to be the same before you run the compare. Try it and see.