Yes v4.0.1.3 has fixed respecting the H264/H265 setting for Amazon. The H265 (HEVC) files are smaller, but if I recall correctly that is because HEVC/H265 is more efficient at the same bit rates.
And so far Jolt and Without Remorse, which downloaded as H264 and 224 kb/s, 84 kHz, 2 Channel E-AC-3 (DD+) audio on 4.0.1.2, they now come down as HEVC(h265) video with 640 kb/s 48 kHz, 6 Channel (5.1), E-AC-3 (DD+) audio.