Depending on the style/construction of the baritone and the seven string; they would sound pretty different. You're right in thinking that the thicker strings (slight difference) and different scale length (also a slight difference, but noticeable none-the-less) will make it sound different.
However the pickups, I think you'll find, will make the most difference. What kind of baritone do you have? What kind of 7 string do you have? The more different these are construction-wise (pickups, wood, manufacturer, etc.) the more you'll notice a difference.
That scale length will come into play when you're tuning a 4th down. Notes will feel/sound "snappier" and cut a bit more on a longer scale length guitar. You'll also afford to be able to go down even lower on the baritone, if that's your thing, before you notice the notes get "flubby" and wildly fluctuate in pitch from their relative slack.
If you typically associate everything with the sixth string, then I can see how you may be getting confused.
It has been years, but in my experience with seven strings, the familiarity will come in time. When you start to increase the number of strings it gets a bit more complicated. Have you tried the seven string with a high A on the top? A small minority of players do this, and that opens you up to the extended range a 6+ string while possibly making it easier to transition from a 6 string instrument.
