The following comments are partly speculation on my part. If someone better informed has factual/experiential information, that would be most welcome.
Combo (VHF comm) + (anything) antennas will tend to be more expensive because:
a) Combo antennas are a low-volume specialty item.
b) Extra measures in design, manufacturing, and testing have to be taken to ensure that VHF comm transmission won't induce significant interference onto the other half of the combo. This may include built-in filters, etc.
So a more expensive combo antenna is not necessarily a better comm antenna than a less expensive plain comm antenna. In fact, even between different plain comm antennas, price is probably not a good indicator of antenna quality.
As for top vs. bottom mounting, it seems like a top-mounted comm antenna may do better during ground operations, and a bottom-mounted comm antenna may do better in flight, simply due to a less obstructed line-of-sight. So as to which should be used for the primary vs. secondary radio, well, it depends on your preferred method of juggling your two radios. But presuming that at least in flight you tend to use the primary, then that would support the argument that the primary should get the bottom-mounted antenna.
But other factors could also come into play. Bottom-mounted antennas tend to be of the bent-whip style, primarily for ground clearance reasons (they also tend to have lower aerodynamic drag). All else being equal, a bent-whip antenna will likely not perform as well as a straight whip due to a higher VSWR as well as being further from the correct (vertical) polarization. But all else is not equal, so as they say, your mileage may vary.
