Yes, there is a very significant difference in strength. That little getrag is the one that gave the 3500 it's bad name in the first place... They fall out of gear, go through syncros very quick, and the cluster shafts blow up with any kind of shock loading. The external slave transmissions can not be fitted with an internal slave cylinder either. There is a machined face and bolt holes for the slave to mount to on the internal units.
Definitely get a 96+ or better yet an 00+ with a 4.8L V8 engine in the newer body style trucks. Much better shifting and way stronger transmissions.