Q: When editing MP4 in Quicktime should you do a "save as" or Export

I have to to do some basic editing in Quicktime Pro of MP4 video. If I do a "save as" the suffix is changes to ".mov." If I do an export the MP4 suffix is maintained but takes longer and may be doing some re-compressing, I'm not sure. In the past I have did a "save as" and merely changed the suffix to ".mp4". But could this cause a problems in certain players down the road?