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Its easy.. You only have to encode the 24/96 flac's to 24/96 DTS with the DTS-HD Encoder (the build in encoder encodes only 48kHz) and put the files in the left collum..
you can easely make artwork from the backside of a disc cover.. Its written in the user guide also.. name the songs and it will show as subtitles.

There is no DVD v or a support for flacs.

For DVD v, you'll need to encode the audio with something. Supported encodings are DTS, or Dolby.

for DVD a, which is an old format that many players no longer support, you'll also need to encode the audio. The supported encoding is MLP.

For 48 Khz there is a free DTS encoder, but for 96 KHz, DTS, Dolby, or MLP, only commercial encoders will have that feature.

Because of the DVD-A format is no longer used the preferred choice for 96/24 lossless playback would be to encode with DTS-HD MA and burn on dvd (or Blu-Ray)

Actually, I just checked, and the DVD-V format does support Liner PCM 2 to 6 channels however:

"PCM: 48 kHz or 96 kHz sampling rate, 16 bit or 24 bit Linear PCM, 2 to 6 channels, up to 6,144 kbit/s. N.B. 16-bit 48 kHz 8 channel PCM is allowed by the DVD-Video specification but is not well-supported by authoring applications or players."

It's not clear to me if 6 channel 96 Khz is "well supported" or "not well supported" nor am I clear on how you would mux that or if PCM = MLP?

I guess I need to have someone answer the basic question...

Can I burn 24/96 FLAC audio files to a DVD-R using AudioMuxer without downsampling from 24/96?

Conversion to 24/96 DTS is fine as long as resulting DVD-V (or DVD-A) disc is playable by a universal player such as OPPO or my Esoteric UX-3 which are both DVD-V and DVD-A capable. I DO recognize that DVD-A is a "dead" format for all intents and purposes.

Yes you can. But:

1) it will need to be in AVCHD or Blu-Ray format
2) A typical album will not fit on a single DVD-R

That's why you need some encoding, to compress the audio.

To experiment, you can use the audio conversion tool in audiomuxer to convert your facs to wav files, then mux those. Audiomuxer will complain if you have an incompatible combination of stuff.

I took an album's worth of 96/24 5.1 flacs (originally from a dvd-a) and did the above. Audiomuxer told my I had to use mkv (AVCHD or BluRay). I chose AVCHD but the resulting folder was 5.7 Gigs. Total Media Theater will play it, but it keeps complaining about invalid disk, I'm assuming because of the size (but I guess it could be dual layer?).