The Cap you speak of was only optional, are department leaves an antenna on the radio, just incase the need to remove the PSM mic for any reason. The older MTS2000 style of radios had a plunger on the accessory port on the side that would switch the RF path from radio antenna to PSM mic. When Motorola came out with the XTS 3000/5000 series the got rid of the plunger and had you to install this high dollar big funky adapter at the antenna port. But basic functiality was the same as the MTS2000 style radio's. Now with the APX it is a different story, there is not a mechanical switch, they moved the RF port back down to the accy connector, but there is no mechanical plunger to swith RF paths. The APX series, senses the device connected i believe through a simple protocol like USB. In the case of a PSM mic with the antenna, the radio know's what it is and swithces RF paths accordingly along with audio characteristics with the type of device connected. Interstingly enough it seems they got this idea from the Motorola Mototrbo series of portables that do the same thing.
Interesting that you brought up using both antennas for improved reception, this is entirly I would say plausable, but I do not know for sure.