When I select Quick Setup Audio Rec on DAW, Part 1 is routed to Main L&R, Part 2 is routed to USB 1&2, and Part 3 is routed to USB 3&4. When I select any other Quick Setup, all parts are routed to Main L&R. Since my Cubase audio track was only getting input from MainL&R, I think this explains why sometimes I was only recording drum audio.

I would have figured that routing like this is something that I would set up myself for each individual Performance. And, in fact, you can edit the output destination for each Part. But then Quick Setup comes in and overrides the audio routing. I imagine this is useful somehow, but I don't get it. I'd be happy for someone to explain what the point is.

The QUICK SETUP Templates are like all templates, useful if they serve your purpose. Just as in the Motif XF with its 16 audio bus outputs via FW, when you selected the default audio template, it set Part 1&2 to the Main L&R, and each successively higher Part to the next available assignable stereo pairing. As I wrote in the article about the "Default Mix" you can and should customize any template so it serves you.

When it comes to the default for audio output assignment, they could have left them all assigned to "Main L&R" and you could change them as necessary when you encounter them; they could have assigned all of them to Part Output "Off" which would force you to choose an assignment; or they could default it as they did... Showing a possible example assignment.

It has to default to something. I can only guess the current configuration, is to alert the user that you *can* assign any part to any output. And I think that's the point... It's just an example. Not a recommendation.

If you route a PART to the "Main L&R" output, it will pass through the System Reverb and Variation effects, the Master Effect and the Master EQ before arriving in the DAW. If you opt to assign it to one of the 30 assignable outputs, it will be removed prior to the System and Master functions, but arrive in the DAW with its Part EQ post the Insertion Effects per Part.

If you wish to render audio for a Part using the Montage System Effects et al, you can isolate that Part and route it through by its self. It's totally flexible. Don't let the default setup template throw you. As I said in the document on the XF "default mix", I've done tons of projects but have never (ever) wound up using the default output setup... It's just a default example... Is all. If you've read my stuff, 'default templates' are dangerous because people can mistake them for mandates on HOW TO WORK... but often they are not that at all... They are just the default examples, please customize.

If they set it with all outputs OFF. It would generate just as many questions... "Why no output when I select the quick set?"
If they defaulted it (as I would) to all channels to "Main L&R" some folks would never find the assignable outputs, again just as many questions. So either way...
By the way, you need to have a VST CONNECTIONS > INPUT Setup to receive each USB OUTPUT you create in Montage, it is seen incoming audio in the DAW.

Fortunately, the "Audio Rec on DAW" template here is a user preference. So if you prefer, recall the "Audio Rec on DAW" Quick Setup template, change your audio PART OUTPUTs to "Main L&R" for each Part, once set as you like, return to the Quick Setup screen touch the box "Store Current Setting"

Store your settings to Setup number 3 "Audio Rec on DAW"
This will be stored as part of your user system settings and will be backed up in your User files.

As to your question about the graphic connection between the word "Part" and "USB1-30":
If you set all the Parts to "Main L&R" naturally the connection between "Part > USB1-30" will disappear, because no such routing is active.

Can we have a firmware update to allow us to save quick setups as a file that is not assigned to the 4 slots on the quick setup menu? I would hate to override the defaults by mistake - maybe they are useful

None is necessary. The factory default can be recalled. They get written in any backup file you create - make a file with factory defaults keep it in a safe place. Also, my recommendation is to learn what these templates are doing. It is not hard, it is new maybe, but it is not hard. Once you look at them - see them for what they are - and realize, "oh, I could set that up myself!" Then you reach a "comfort zone" with the product, that lets you relax and navigate like a pro. You want to be in that zone.

The one template that is meant to be and MUST BE customized by you, is the audio recording template. No one sitting in an office at Yamaha has a crystal ball that could predict exactly what Parts you want to route to separate audio tracks in Cubase - there are 32 totally configurable outputs. You make that choice as your OWN production decision. While there is a MIDI RECORD template that works for most every normal MIDI record situation, and while there is an ARP RECORD template that works for most every arp record situation... For audio, expect to customize that setup!

If ever you want to restore the factory setup and you don't know how... Simple initialize the system settings to recall the defaults. (but at that time, say to yourself, "I should really take the ten minutes to master this template thing like Bad Mister said" - and then Just do it!

Hope that helps and inspires!