This is a topic that has bounced back and forth for years. There are those who love rubber cement and those who don't. Good thing there is room in the world for all opinions. I like both methods and choose the one that I think is most appropriate for the application I'm working on.
I use the RoS dies to cut either freezer paper templates which I iron to the wrong side of my fabric and then add the seam allowance by leaving 1/8" to 1/4" of an inch around the shape when I cut the fabric. If I'm doing fusible applique I attach the fusible web to the wrong side of my fabric and then run four layers through my AccuQuilt cutter.
Our stencils do not include a seam allowance either. I use them to trace the shape either on freezer paper or on the carrying paper on fusible web. With freezer paper, after I cut out the shapes I do the same as I would if they were cut on the AccuQuilt die. Add the seam allowance when cutting around the shape after it has been ironed to the wrong side of your fabric. Fusible applique is done the same way with shapes cut on the AccuQuilt die or the 'old fashioned' way.
To answer your final question Fran - the residual rubber cement does not wash out - and so far I've not had any deterioration as a result of it. However, I've only been using it for 25 years and I can't guarantee it for longer than that. At my age I don't really care what happens to it after that. LOL