Marked caliber comes into play when you're registering a Short Barreled Rifle. After you have the stamp for your SBR 5.56 rifle, you can legally mount and shoot a short barreled 300BLK upper if you want - but you better not get rid of the shorty 5.56 upper. If you wanted to permanently convert your legal 5.56 SBR to 300BLK, forever, you better be sending in a form before you do it.
Otherwise, it doesn't matter.
On a state-view, it all comes down to pistol config. Some states require your AR pistol to be on a marked pistol lower. Research that for your state.
Otherwise, it doesn't matter.