Line out - Yes. Line out is when you want to take a signal from your DAP that doesn't pass through the amplifier of the player. For example, ipod. If you want sound from an ipod, you can connect the 3.5mm cable to an amp, but this is using the ipod's DAC and AMP. If you use the 30 pin line out (I'm old school - No lightning connectors here) then you can get the sound directly off of the DAC and output "line-level" to an amp. Line level volume is usually not variable and is what is needed for an input to any amp, receiver, etc.
Line out differs from USB out in this way. Line out is an analog signal that is set to a level volume that the amp is looking for. USB Out is supposed to be a digital bit perfect output that will need to go through a Digital to Analog Converter (DAC) for decoding.
(Personal opinion here) I used to listen to my iBasso DX50 with Line out signal into my RSA Intruder AMP. When I got the N3, I connected the USB out of the N3 into the DAC input of the RSA Intruder. It is my opinion that I heard better sound and wider soundstage by using the RSA DAC rather than using the DX50 to decode. That is why I bought the N3 immediately upon hearing the demo unit. Because to me, the soundstage and presentation of the USB out was better than the DX50 Line Out.. (Personal opinion over.)
Folder Play - Yes. You copy songs and folders over to the micro SD card like in a computer. The N3 and M2s can scan your micro SD card and add the files to a library. Then you can use the "Artist" category to search for your music, or "album" category, "genre" etc. Since I just copy over artists and their albums, I just select the music from the directory structure. = Folder Play.
Dual DAC - Theoretically supposed to be better with one DAC for each side of the stereo presentation. But I have not yet owned a dual DAC player. So not going to comment on better or not. I'll let someone who experienced the DX90 or another dual dac player jump in here.