MKV subtitles converting to M4V problem

[pcs2922]

I've ripped a DVD to a lossless MKV file using PavTube Bytecopy. I want to convert all the audio and subtitle tracks to M4V file to watch the movie on AppleTV. The audio tracks get converted fine, but the subtitles are the hiccup. I can only force or burn 1 track, but I want all the subtitles to show up as options. They are VOBSUB bitmaps, and are greyed out, so it seems Handbrake is not recognizing them as a compatible output. But on the handbrake documentation is says that for MKV's multiple subtitle tracks can be "passed through." Pardon my ignorance, but I don't know what this means. Can I get all of these subtitles tracks to come through as choosable options in my output file using Handbrake or no?

I'm using Handbrake 1.0.2 and OSX Sierra 10.12.3

http://pastebin.com/FFv9YsMX - This is where I have pasted the log activity.

[rollin_eng]

If you have mkv as the output, yes.

[Ritsuka]

What's grayed out? There is nothing preventing VOBSUB in mp4 in HandBrake, I see you successfully copied them in the mp4. Just keep in mind QuickTime doesn't read them. You need to convert them to a text based subtitles format, for example with Subler.

[pcs2922]

So, can Subler extract the subtitles and convert them from the MKV? Or do I need a more than one program to do this? I'm looking for the simplest way to get these subtitles from the MKV file to work in iTunes.

[Yogui]

Hi,
Has anyone found a guide to do this? I'd love to be able to enjoy my iTunes library from the AppleTV and to be able to choose the audio and subtitle tracks on the fly, just like with a DVD or with a VOD service.
At the moment I'm encoding with HandBrake to M4V files, since they seem to be best when there are several audio tracks. The subtitles show up just fine with VLC, but with iTunes I can only change the audio track (not any subtitles).
Thanks!