Actually there is very little difference. Medical glue will actually dissolve more slowly than craft type superglue. The active ingredient is cyanoacrylate, the medical version is actually 2-octyl cyanoacrylate which is primarily less toxic and irritating than methyl (or ethyl) cyanoacrylate. The solubility when used internally for wounds is typically days so using it as described is totally stupid unless you enjoy spending the evening in your local ER.
Playing with superglue is an advanced kink and requires a great deal of care, external use only. If you glue your finger to your dick at least its not going to kill you, blocking your urethra could.