What they are saying is that you will have to access the dvd menus to change settings if you hook it up the way you intend and that will be quite a bother and they don't recommend it.
When playing DD/DTS you have two options: Bitstream or PCM. If Bitstream, the signal is sent as a stream of bits that the receiver will decode. If it is set to PCM (or OFF, whatever your player menu says), the dvd player will do the decoding and downmix it to 2 channels.
Now, if PCM output is ON, then after decoding, the dvd player will send the 2 channel mix out the digital out. If PCM is OFF, then it will do digital to analog conversion and use the analog outs. So you will have to change that PCM setting everytime you want to use the analog outs.
In contrast, there is no problem using both optical and coax digital outs if the player has both and connecting one to the dvd input and one to the cd input on the receiver (without changing your menu settings).