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Ah but nothing stops you from editing the HTML file before you process it with an automatic tool. There are a plethora of nice little GUIs you can use to do that.
The downside of having an all-in-one tool is that it can never perform any one function as well as a single purpose tool. It's kind of the difference between the Unix and windows philosophies.
Another important point is that LRF is not a good archival format. Like PDF it needs to know the screen geometry and DPI for best results. You really don't want to have to put in all that work you do in cleaning it up on the LRF.
HTML or some dedicated XML semantic format is much better for archival. The proofreading work should go in there, not at the LRF stage.
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