Even if Denon rates their receiver wattage more accurately that really isn't relevant. What is the difference between 100 watts and 80 watts? Well I will tell you, it is about 1 decibel.
What is a high current amp anyway?
An amp is an amp. It's power is determined by the sum of it's parts. The amplifiers in the Yamaha HTR-5990 are quite capable. They have a large power supply, plentiful capacitance and a hefty output stage. I have no doubt the amplifier in the Yamaha is just as good as the one in the Denon or any comparitive receivers that you listed.
The argument for 1.3 and all that stuff is a dead horse. LPCM should be just as good as DTS-HD or Dolby TrueHD, the only difference that it makes is that it is decoded inside the dedicated player instead of a receiver.
Lastly, If a reputable receiver manufacturer states the receiver processes 7.1 LPCM you better bet you buttons it will process 7.1 LPCM. As for the processing capabilities compared between the Denon and Yamaha, they should be almost the same, probably not audibly different.