What does MakeMKV do differently than eac3to?

[bitfidelity]

I just had a strange experience with the newly released Gladiator UHD: when I use Clown_BD (which utilizes eac3to for demuxing streams), I end up with an MKV where the DTS-HD MA track is noticeably out of sync throughout the entire movie. MakeMKV, however, manages to create an MKV without issue.

Does anybody have any idea why eac3to would fail, while MakeMKV doesn't? I suppose the issue could have something to do with mkvmerge, which is what I use to actually create the MKV when I use Clown_BD/eac3to, but I really think the issue stems from the latter, as it creates a log with many audio gap warnings such as these:

[a04] Audio has a gap of 31ms at playtime 0:16:23. <WARNING>