I pasted a table from MS Word with and without the processing that your system offers. The table worked in either case and I think it looks better with all the Word tags left in place. The point is that, apparently, your filter removes some tags that your engine can correctly render. I would think that, ideally, the only noticeable difference would either be that a paste had to be filtered in order to work correctly (which I've also seen) or that the filtered HTML is simply smaller with no change in the appearance of the rendered page.
Are you planning to improve this processing in the future?