I dont think painting it is a good idea, with time and wear the paint will look pretty bad. I had this happen with a paver patio before. I had an extension made to our patio and when we used the new pavers for the extension (it was the same brand and color as the old ones) it did not match. The installer did a great job by suggesting we remove some of the old pavers and mixing in some of those pieces with the new patio. That worked great! Maybe that can be done here, removing some of the old cobbles, mixing in new ones with old ones.

I think it’s a slightly wider mortar joint and wet/ uncurled mortar versus dry. This will age in soon enough to where it won’t be so obvious. You won’t be happy with paint.

I think Hallett is correct. Raj Kumar has a great idea also.

There is stain (rather than paint) that you may be able to use.

Another suggestion (if you are going to rip them off anyway) is to buy a contrasting color to make the difference look intentional like an accent point.

I think it will age and soon not be so different. I think trying to"fix " it could be worse . I has a purpose so IMO just let it age .

Is your driveway, then, gravel after this transition? I would think of the section you just installed AS a transition piece from your threshold to the driveway. Over time, as the mortar dries and lightens in color, it won’t be as obvious. Wear and tear will also do their “thing” to the middle section, but think of it as a transition, NOT as part of the threshold. Yes, a mind game, but sometimes helps to bring yourself around to accepting what you think of as a “flaw.” It isn’t.

I think your cobblestones look like granite and that will not take a stain and paint will peel off over time. It might have worked better if some of the new batch had been dispersed through the old batch.

Has the installation been power-washed to eliminate all the surface dirt????

Your granite stones might take an enhanced sealer. They come in different sheens so don't select anything shiny.