I have also been working on remuxing War of the Worlds. Regarding the seamless branching issue,
this thread makes the case that eac3to produces reliably accurate demuxed DTS-HD MA tracks from discs with seamless branching.
To test this, I first ripped the WOTW 2010 US BD directly to an MKV file with MakeMKV, and extracted the DTS-HD MA track from it.
I then used MakeMKV's "backup" function to rip the entire disc contents of the BD, and this time used eac3to to extract the DTS-HD MA.
I compared the two files in foobar2000 with the Binary Comparator component. It reported that the two files have differences after the first branching time at 2:41. Also, the MakeMKV audio was 10ms longer than eac3to's. So you do indeed get different results depending on which program/method you use.
Taking the experts' opinions that eac3to's audio should be the most accurate, perhaps using its demux of the BD audio will produce better sync when remuxed with the UHD video. I will try this today.
(Side note: I found that the US BD uses seamless branching, but the US UHD does not.)