The 5-103669-2: The through-hole mounting with press-fit or solder termination gives you flexibility: press-fit for high-reliability backplane assembly where rework is rare, or solder for prototyping and field repairs where a soldering iron is on hand.
Peer Comparison: 1394090-1
The closest functional alternative in the same family is the 1394090-1, a 6-position right-angle header with 0.112" (2.85mm) pitch and thinner tin plating (39.4 µin vs 100.0 µin). If your BOM calls for 3 positions and a 0.100" pitch, the 5-103669-2 is the direct match — the 1394090-1 requires a board layout change and a different mating connector.