My friend and I have narrowed down a peculiar issue as this: When ripping SD PAL 16x9 video off of blu-rays, the DAR gets all mixed up. Instead of taking the 720x576 stream and displaying it at 1024x576, like it ought to, it gets displayed at 1047x576, slightly wider than 16x9. This does not happen with 4x3 PAL SD content, and it does not happen with SD PAL 16x9 content ripped from DVDs.
I'm not sure what the cause is, but it's not a MakeMKV bug specifically - even playing the videos directly off the blu-ray in VLC causes this overstretch.
The issue seems to be rooted in the absurdly annoying and complicated SD broadcast standards, regarding pixel aspect ratios and horizontal blanking intervals, and 720 vs 704. Seeing as no discs I've ever seen care about or use the blanking space, I think it would be cool and nice if MakeMKV proactively fixed this peculiarity when ripping 16x9 SD PAL content and ensured the resultant file had all its metadata set to 16x9, and instead of a pixel aspect of 16/11, go with the pixel aspect of 64/45.