The distinction, before about 1998 or so, was pretty much immaterial: Totally Games was "independent" but was composed of ex-Lucasfilm Games people and only published through LucasArts. I cannot say for sure, but I wouldn't be surprised if Lucasfilm (then LucasArts) had an ownership stake in it at one point, as Nintendo did with Rare during the mid-90's.
Contrast this to, say, Raven Software doing Jedi Knight 2 and Elite Force right on the heels of one another. (Of course, Totally Games did do Star Trek: Bridge Commander, but that was seven years after they split from Lucasfilm Games.)
Contrast this to, say, Raven Software doing Jedi Knight 2 and Elite Force right on the heels of one another. (Of course, Totally Games did do Star Trek: Bridge Commander, but that was seven years after they split from Lucasfilm Games.)