The universal players have 5.1 analog outputs because Toslink and other SPDIF formats cannot transfer DVD-Audio and SACD audio media, the brandwidth is higher on those mediums and SPDIF has limitations. The audio for DVD-Audio and SACD is decoded inside the player. Some Universal players have Firewire ports that can be connected to designated receivers and processors that feature Firewire connectivety. HDMI can also be used to transfer DVD-Audio and SACD to a capable receiver or processer.
The only usage you will get out of the SPDIF outputs are 2 channel PCM (CDs mostly), and bitstream from standard DVD (Dolby Digital, and DTS tracks).
There is no problem with using both connections.