Hi lemarrc,
Yes, the volume boost is applied during playback (that's why it's under the "Playback" tab) of Preferences.
You could manually boost the volume in the recording external to Pear Note as you suggested, but as you said it will be a pain. If you choose to do this, I'd suggest not digging inside the Pear Note document package. Instead, I'd export the recording as a .mov, increasing the volume in some audio editor, then import the recording back overtop. This way you don't have to deal with the possibility that Pear Note internally split the recording into multiple files.
I have to say I'm surprised simply turning up the volume is not sufficient for your purposes. The microphones on all these devices certainly are not high power, but they're usually sufficient for most uses.
I'm not sure what you mean by "issues while transferring recorded audio". If I didn't cover it, please explain what you mean.
Thanks