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When you re-encode properly, you aim for transparency to the source. When you abide by lvl 4.1 rules that isn't always possible. Simple really.
Say you're reencoding a Blu-ray with x264. The way the information is presented (video) varies extensively throughout each and every Blu-ray. Some video might only need half the bitrate of the source using certain settings while another might need double at the same settings. Same goes for the number of reference frames (which the one of the main factors in determining level). One source might need more than the source, another might not. Granted, set a high enough bitrate and you could use the worst settings possible and still achieve visual transparency, but that's not the point.
The point is.. just because the source is done a certain way doesn't mean changing the information in such a way to BEST represent the original one (reencoding) constitutes restricting options for how that information should be manipulated, a la using 'worse' settings. With that said.. no, there is nothing wrong with having a reencode have a different level. Sure, having the same level would probably give more benefits than not, but it still doesn't mean that it can't or even shouldn't be used.
To achieve transparency, it might help to use more reference frames than are supported by L4.1?
Also, I wasn't saying L5.1 is never useful. I was just under the impression that it isn't useful for Blu-ray sources.
It definitely is useful, but the benefits of using it (achieving minimal gains in compression) versus not (hardware acceleration on most platforms) are pretty one sided.