Interestingly, if you set MeGUI to encode to MKV container instead of MP4, everything works fine. No vobsubber, idx files or anything like that needed, it gets everything from the IFO and muxes it correctly. Unfortunately I have to have MP4, but I guess I could convert that later with some other tool. Since we're digging around I thought I'd give it a shot.
All this does pose a bit of a worry for me though, should I get my hands on any blu-rays. I've come across one in the past that did need detelecine (or deinterlace, I forget which it was), so MeGUI would be the preferred route. MakeMKV is the only thing I know of to copy a blu-ray disc, which would more than likely invoke L-SMASH or FFMS again. I wonder if any audio/video desync issues could arise there...
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For MKV, MeGUI doesn't appear to specify a stream when muxing subtitles, so everything in an extracted idx/sub file would be muxed and it's clever enough not to mux empty subtitle streams. If the first subtitle stream was empty though, it wouldn't matter. I haven't tested the OneClick encoder to find out if it only extracts the single subtitle stream it displays, or all the subtitle streams if there's more than one.
Every Bluray video I've seen was progressive. That doesn't necessarily mean anything, but the only interlaced/IVTC Bluray content I've come across was in the standard definition "extras". The Bluray spec says for 720x480 it has to be 59.940i. From memory in one instance there wasn't much effort put into it. Some of the extras were simply progressive 23.976 with every fourth frame repeated for 29.970fps and encoded as interlaced.... or something similar. That was a fair while ago though so my memory is vague.
I haven't ripped any Bluray discs for a while but normally I'd run AnyDVD HD in the background decrypting and rip with MeGUI's HD Streams Extractor (under the Tools menu). It extracts the video stream to an MKV. Apparently AnyDVD is no more and I haven't investigated any alternatives. The DVDFab equivalent is called DVD Passkey, but it's not free. I grabbed a copy when they were giving it away as part of a promotion but haven't actually used it yet.
I wouldn't worry until you come across a problem video, and even though I live in PAL land, I'm pretty sure interlaced/IVTC would be pretty uncommon for a main Bluray movie. Unless it's old NTSC video or something....
If it is I guess there's a potential for the same sort of problem, but it's fixable. You just need to tell ffms2 or L-smash how to decode it properly. Cross that bridge if it happens, or if you're keen there's DGIndexIM or DGIndexNV. MeGUI supports them and probably includes them in it's Tools folder, but they're not free. Not expensive either.... $15 or something like that. I haven't paid much attention so I don't know exactly what they support but I believe they'll index MP4s and MKVs and they understand AVC, VC1, HEVC and mpeg2 video. The HD equivalent of the old DGIndex. http://rationalqm.us/dgdecnv/dgdecnv.html
You could possibly rip a DVD with Make MKV and index it with one of them.... I'm not sure though.
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