For 2-channel systems I was thinking of a Marantz PM 6006 or Cambridge Audio CXA60 (I like this because of the bluetooth option for streaming). In this case I could take advantage of FLAC files (I dont have many but could grow this collection) with the built in DAC"s.Both are very good integrated amps and will do a far better job with music than any AVR could.
No, it will not sound as good. AVR's are built primarily to decode, process and amplify signals from digital sources. AVR's are all about features and not about hardcore audio performance. The biggest reason being their preamp sections. These are just a mere afterthought, even in so called pure direct mode, and usually comprised of a few op amp chips. The preamp sections in a quality integrated amp uses far more discreet parts resulting in much higher level of musical performance before the signal is sent along to the power amp section.
if I went with HT amp I was thinking of an SR5011 because I like the streaming options and easy remote app. My main concern is if I go source direct with this amp, will it sound as good as an integrated 2-ch amp around the same price level?
And finally, speaking of the power amp sections - don't get misled by the power output figures that AVR's boast. Either the PM 6006 or CA A60 will kick the SR5011 to the curb when it comes to driving a pair of speakers. And this an amps first priority - driving speakers. Everything else is just a feature.
If you don't need surround capability, and it doesn't sound like you do, stick with 2 channel stereo components. Especially with vinyl. Digital sources can still be enjoyed too. That's why a DAC is for.