"i was always warned that jewlers rouge can get into the metal pores and stay there"

Not true. Been using jeweler's rougeintwo grits for 40 years.

I am fairly new to Mls and I've read alot of posts about JB bore paste.
Before getting into the blackpowder side of things, I only shot and hunted with centerfire and rimfire rifles and pistols, so this is where my experience lies.
One of the things I was taught as a lad in Alaska regarding guns ( by my Grandpop and my Dad) is that they almost considered it a sin to put an abrasive down a rifle barrel. They used bore brushes infrequently and depended on good solvents to eliminate fouling.
Maybe it's that age old Scots/Irish thing about trying to make a tool last a lifetime rather than purchase again. It seems to me that using any abrasive would be the same as a few hundred or a thousand rounds through that barrel, and in doing so, shortens the life of said barrel.
I don't know. I do know my Grandpop wouldn't part with a nickel if he could help it.
Not trying to be contentious, just don't completely understand the reasoning I guess.

I guess my question is,... are new muzzleloader barrels that much rougher than a center or rimfire barrel, that it has to be polished before it'll shoot right?

I think if you check there are a lot of people that use the bullets with abrasive on them to break in new centerfire barrels. It sort of depends on what you think is required to "break in" a barrel. In the case of the muzzleloader a lot depends on how the rifle loads which is not part of the centerfire routine. My Omega was a bit#@ to load and polishing with JB made the loading a lot easier. All rifle barrels have some machining roughness remaining. Probably the cut ones are a little worse than the button rifled ones but again it is sort of your decision. As I mentioned before just a lot of shooting solid lead bullets will eventually break in your muzzleloader. Doc White says to not be concerned with how your rifle shoots until the first 200 loads. Thats a lot of shooting for me as I have trouble getting that much range time. With four new rifles last year that means 800 rounds.

I see your point.
For a competitive shooter, or someone concerned with how tight he can get the groups on a target, that makes sense. Every rifle I have ever owned, I can sight in and be happy with out of the box. I never have been concerned with MOA. I'm not exactly the poster boy for benchrest shooting.
For you fellas that want to do it, more power to ya. Just can't see it myself.