The incompatibilities still exist at least in Windows sistems, since
LyX installer bundles a python distribution itself and creates a
conflict when python3 is the default. Moreover you cannot use python3
within LyX in Windows, because you will beak the system, LyX will not
reconfigure anymore!!
Just my experiences
LyX 2.1.2, Win7x64, Anaconda 2.1(python 3.4)

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