With the 50w, yes I do use the Blue channel primarily, but boosted with a Boss GE-7. I boost the overall level of the Boss GE-7, just a flat boost. I find the channel saturates best that way, and retains its dynamics if you're good with your right hand and the volume knob. The Red channel is fun to play at home at low volumes because of how compressed it is, but that limits how expressive and clear it is at higher volumes. The Blue channel is definitely the winner of the 50w 6L6 in my opinion, boosted or not.
To your point I have also read that the 50w's Red and the original 100w 5150 III's Red channel are identical, as that was one of Eddie's specific requirements for a 50w version of the 5150 III. Also, I have A/B'd these two amps and can confirm that at non-poweramp-saturating volumes, and with use of the 50w's Depth control, the Red channels of these two amps can be made to sound and feel identical. I've done it.
However, comparing the Red channels of the 50w 6L6 with the Stealth 100w, the channels are not identical. The Stealth 100w's Red channel sounds better to my ears. I'm sorry to say I cannot explain exactly why. It just sounds "bigger" and clearer at the same time without losing saturation, regardless of the position of the Depth knobs. It is absolutely excellent and in my very humble opinion, the best pure high gain channel in the entire 5150 family.
As far as the Blue channels go, again you're correct that the 100w Stealth's Blue channel is actually not quite as tight as the 50w's Blue channel. Basically the 100w Stealth feels like it lets in just a bit more low end into the preamp. I think the Stealth's Blue channel feels just a bit more saturated overall than the 50w's Blue channel due to the increased low end allowed into the preamp gain stages. Boosting the Stealth's Blue channel with a Tubescreamer-esque or low-cutting EQ curve is where it's at here. However it's more compressed than the 50w's Blue channel. With the Stealth 100w, the boosted Blue and non-boosted Red channels are equally fantastic, but different flavors, for the modern high gain thing. Comparing the two amps' Blue channels, it's hard to put a finger on describing the difference between the two but if I had to come up with something, I'd say the 50w has more of a snarly, hotrodded 80's Marshall "guitar gunslinger" vibe to it, while the boosted Stealth 100w has more of a "standard" modern high gain vibe.