The 6.5CM might not have a higher b.c. it's partially about comparing b.c data across bullets of same or similar sectional densities. In the example you gave, s.d. is not as close a comparable to then look at other ballistic data. For instance, you can handload the 270 win with 130gr CEB bullets with a .540 b.c and still get 3100+ fps. A lot of .264 bullets of similar sectional density do not have as high a b.c. and of those that do, say, a similar 120 gr CEB bullet, velocities are likely going to be closer to 3000+fps
in the 6.5 CM andd b.c of .500 vs . 540. with the 270 win..
To your question, all else being equal, the better b.c, bullet will eventually compensate for lower velocity over time (distance) versus a higher velocity bullet of lower b.c. .
"Does higher BC factor into how the bullet will perform when it actually hits the target?" in part, yes. the higher b.c bullet might have higher retained energy and may help you have more leeway in guessing wind drift...but most important will be final bullet placement and bullet construction that will determine how it will perform.
