Well, for one thing the Yamaha could only apply that enhancement when it was doing the decoding of the Dolby Digital or DTS signal. In other words, it will only work with the multichannel analog output. The digital output goes straight through the player to the 990 with no processing by the player. Likewise, settings in the player like speaker distance, bass management (large/small speakers), and channel trim will only affect the multichannel analog output - and with the way the 990 handles the 7.1 Direct input, they can all be "zeroed" out (no delay for speaker distances, no trim on speakers, all speakers large and sub on) as a general rule.
Based on my experience with a Yamaha DVD player (the DVD-S1500), I suspect that going straight to the 990's DAC's will sound the best. If you'll be connecting multichannel analog anyway (perhaps for DVD-Audio and/or SACD), you could still do a comparison between digital input, multichannel input without "Cinema Dialogue," and multichannel input with "Cinema Dialogue."