Manuscript Revision: Is it alright to include the response to reviewer comments as an attached file rather than typing in the text box provided?
Speaking as an editor, I don't care whether you put text in the box or upload a separate file as long as what you provide is clear.  Speaking as an author, I have done it both ways many times, and it has never made any difference.  Generally, if the response is relatively short, I'll put it in the box; if the response is long or uses significant formatting (as in your case), I'll attach a file instead and put "See attached comments" in the box.

In short: they wouldn't provide the upload option if they didn't want you to use it.