Some people have done this successfully in the past for the same reasons. Its cool that you've thought of it on your own.
I cannot think of all the potential problems right at this moment. I think you definitely want to make sure that you don't have a site included twice in different instances/layouts of SaT. Make sure a site is only included once. Also, for the hotkeys, if you want them to work across all instances, you probably should use the ~ prefix for each keyname so that SaT will pass the key through to other instances. That' all I can think of for now.
I cannot think of all the potential problems right at this moment. I think you definitely want to make sure that you don't have a site included twice in different instances/layouts of SaT. Make sure a site is only included once. Also, for the hotkeys, if you want them to work across all instances, you probably should use the ~ prefix for each keyname so that SaT will pass the key through to other instances. That' all I can think of for now.