Why doesn't T5 exonuclease have endonuclease activity in Gibson assembly?
The buffer conditions used in the reaction also mitigate against the endonuclease reaction, so it should not be a problem if you stick to the protocols exactly. I've worked on this enzyme since 1988 and was the original "cloner' of the overproducer see http://www.sayers.staff.shef.ac.uk/fen/   for more information on these enzymes
Jon Sayers, University of Sheffield.