I have never liked the idea of cutting the string itself past the windings. I know Mike Watt does it on a regular basis with his short scale, but he almost always uses D'Addario rounds.
There are a number of short scale flats available. I would suggest these websites to find them:
www.juststrings.com www.bpstrings.com
You can also get a few sets from musician's friend as well.
Some of the companies (off the top of my head, there may be more) making short scale flats are GHS, D'Addario, Rotosound, and Thomastic Infield.
