After some digging and testing, I think I understand where I went wrong.
If someone would be kind enough to confirm that my understanding is correct and correct where it is in error.
There are essentially 3 subtitles types and what I'll call a pseudo-type (There are other subtitles types but I haven't encountered them yet):
VobSub, CC (closed captions), SRT, and the pseudo-type "Foreign Audio Search"
My understanding of how the iPad 3 and HandBrake interact with these is as follows:
- VobSub: I can only use "Burn-in" (aka Hard) with this. The iPad (*.m4v) won't recognize this as a subtitle track; therefore, there is no way to select these as soft-subtitles.
- CC: This works fine as a non-"Burn-in" (aka Soft) subtitle track. It is recognized as a subtitle track (vs CC) by the iPad, but I don't care about that.
- SRT: This would work as a non-"Burn-in" (aka Soft) subtitle track, if I go and find my own SRT file and then import it into HandBrake (which requires too much work for my-lazy-self). Also, some people seem to have issues with the entire line of a given subtitle being cut-off. For example, if the subtitle line is "Jack and Jill went up the hill" only "Jack and Jill went u" may be displayed. This seems to be correctable by editing the SRT file.
- Foreign Audio Search: This shows up for all DVDs but may not really exist. It is the "English" (for me) subtitles you would normally see if subtitles were turned off and a character spoke a foreign language. If you select this, you'll get those subtitles "Burned-in" to the *.m4v. If there are no foreign audio subtitles (i.e. everyone speaks English), you'll get nothing. Not sure about how this interacts with a burned-in VobSub or CC.
- Pick CC, if it exists, and don't select "Burned-in";
- If no CC exists, select the English (VobSub) and select "Burned-in" (which will result in hard subtitles, but it is the best I can do for zero extra work); and
- If neither CC or VobSub is available, I can either try a "Hail Mary" with Foreign Audio Search or go look for a SRT I can import.
While I am posting I'll also add, the iPad 3 (at least) can handle multiple audio tracks (e.g., Japanese & English, normal & director's commentary).
Thanks for the help.