The E4OD itself went through a lot of evolution and from my understanding the 4R100 just continued that. I know when my E4OD was built, it was updated with 4R100 internals, six-pinion billet planetaries and such. ATO claimed I couldn't hurt it, and 20 years later that's stayed accurate.
There's a bigger difference between the '93/'94 E4ODs and the 4R100 than the '95, which was rollerized and had more substantial bearing supports. So, in short, if you plan on substantial power, it's worth getting a '95 updated. If not, it's already about as tough as a 4R100.
@BONESTOCK and
@FlatOut have both converted their trucks to manual (and plenty of others). If I ever have a transmission issue with my '94, I'll swap it. I'd love a 6-speed in it.