Can a SONY HXR-NX30U camera record two external audio inputs?
Pages 41-43 of the HXR-NX30U manual tells you exactly how to do this.

First of all, the "superdirectional boom mic" is an accessory that overrides the "builtin mic" (which is much smaller and not a boom mic).

Secondly, if you want to use both the boom mic and a lapel mic, you definitely need to use the XLR adapter, which will override the builtin (non-boom) mic.

If you set the switches correctly so that the boom mic is going to one channel (perhaps Ch 1) and the lapel mic is going to the other channel (perhaps Ch 2), then yes, both channels will be recorded to the media file that the camera records.  And iMovie will see both channels within the clip.  You might have to fight with iMovie to explain that the audio is dual-mono, not stereo, but that's an iMovie question, not a SONY question.

Make sure that if your microphone needs phantom (+48v) power, that phantom power is enabled on that channel.