will they be painted?

Just some thoughts
What was on the written quote (did you get a written quote?)when the work was discussed, replacement implies replace with same, repair may not involve replace with same but equivalent.
Lintels are structural items required to support the load from above. Unless the stone can be shown to be structurally sound for this purpose (i.e. no cracks or flaws that would endanger its strength then the builder (or BC since replacement of a structural item may involve BC??) may be reluctant to fit a stone lintel. (I have absolutely no idea how you could show stone lintel to be structurally sound)) The metal strip to which the builder refers may be a metal supporting lintel to make the stone lintel non structural and remove the problem. A concrete lintel will not have these problems as it can / will contain re-bar to allow structural loads. The sill has no such problems as this is non structural.
I can understand that the builder would not want to guarantee the stone as this is a natural product over which he has no control but he should guarantee his work of installation if not the stone.
Will the stone split? Well look at the local cemetery to see how many gravestones have split noting of course the different types of stone. Stones will split due to impact or frost damage, usually on a fault line, so we are back to the problems of the stability of natural material.
You could make an agreement that the builder installs the stone guaranteeing his work but you take the liability for the stone.
Peter

from memory, BS for lintels does allow for some tensile strength allowing it to perform as a beam. alternatively it can be assumed to perform as a shallow arch.
these are design mechanisms - stone lintels have been used extensively in the past but it's neither the ideal use of stone or the ideal material for the job.
artificial stone, which is concrete using "nice" aggregate round the faces, is commonly used and looks like a fine-grained natural stone when installed.

Round here, in Wensleydale, every one uses stone lintels. Sorry just remembered about my Brother-in-laws bungalow this has concrete lintels and the cover is flaking off and the steel (now rusty, is exposed). Apart from said bungalow, every one uses stone also the buildings are made with stone so the weight on the lintel is also much higher then with a brick construction. A lintel only carries the weight of the triangle of "wall" above it, so you can test one, by you and a mate standing on one! Typical dimensions over a window opening of 40" is 6" thick X 15" deep with a 6 " overlap at each end.
Frank