Here is what I do, and it works just fine, though it does take a bit of extra disk space. When I want to run an 'extra' instance of SE, I locate my configuration directory. Say its, "C:\Users\Me\Documents\My SlickEdit Config\17.0.3". I then copy that to a new location, say "C:\Users\Me\Documents\My SlickEdit Config\Alt\17.0.3". I then run SE, not only with +new, but also with +sc, to use the alternate configuration location. So my command line looks something like
"C:\Program Files\SlickEditV17.0.3 x64\win\vs.exe" +new +sc "C:\Users\Me\Documents\My SlickEdit Config\Alt\"
Note that the +sc location does not include the "17.0.3".
This way there is no conflict at all, with config files, nor with global tag files. It works well. The downside (or upside, depending on your point of view), is that configuration changes made in my alternate SE instance don't apply to my 'normal' SE instance.