[Ghitulescu]

Originally Posted by hello_hello

I'm not over-thinking anything. I'm trying hard not to think about your logic behind having to convert formats that you claimed were being decoded correctly.

It is a behaviour at you NOT TO understand what is written. I mean to try to twist what has been said in order to make you like having right when you're obviously wrong. I changed the player and the DVD-A was not supported in the new one (although some reviewers mentioned it). DVD-A and SACD are rather dead and toys implementing both are rare. It is my fault for not double checking this. Since I own olny a few DVD-A discs I decided to convert them to a format my new player accepts, either a DVD-V with lossless audio, or a collection of FLACs, rather than to buy a new, universal player, matching my existing rig.
But when the pieces of gear work - they work. They can't afford to wait for a firmware upgrade or to ask for downloading of a new codec or codec-pack as on a computer. They have to work right out-of-the-box. Besides, a 4.1 DVD-A disc would not be sold if this combination of channels would be unsupported by the players it is designed for.

Originally Posted by hello_hello

According to Table 42 on page 61, the 4.0ch configuration definitely contains two single channel elements.

Table 42 reads, for 4 channels, the following and only configuration
4 ¦ 4 ¦ single_channel_element(center front speaker), channel_pair_element(left, right center front speakers), single_channel_element(rear surround).

So it's a 3 center front-speakers and a single rear one configuration. Hardly a real-life configuration (unless one implements true L and R to be stored as LFC and RFC). This is how I read them. I am not sure this configuration has anything to do with your expectations of a 3.1 configuration (most probably L, R, C and LFE).
But this are the implicit/default matrixes. In other words, if you send a 4-substreams file to any AAC-encoder that encoder has to use the default matrix (table 42) to assign the channels.
If you don't want this stupid 4-chn matrix you have to use a custom assignment, as per clause 8.5.3.2. Wherein

Any SCE’s except the last SCE must be paired, and the presence of exactly two SCE’s (alone or preceeded by a CPE) indicates that the two SCE’s are Left and Right Rear center, respectively.

So, you may have: CPEs (already paired) and paired SCEs but only the last SCE in the list may be a "bachelor" (usually LFE).

Because LFE always was a single channel (since Dolby implemented it in 1991).

Why this strange pairing? For encoding economy - in short, pair channels may be encoded as MS (Mid+Side), known as joint stereo in MP3.
Single channels are reserved for channels carrying important information, like L and R, although they can also be present as a pair (probably to allow an even lower bitrate).