I have concatenated vob files myself in the past without issue, so assuming the format hasn't changed significantly, it can be done. However you do raise a good point, so let me explain a little more without making it sound complicated (because it's not) hopefully...
Originally Posted by thg
With movies, you are likely to have one large or a few large vob's containing the whole movie, a small vob or two containing the menus and another bunch of small vob's containing the extras separately. It's pretty easy to tell just by the file sizes. Just delete the vob's you don't need and concatenate the rest since the extras are in separate vob's from the main movie. Basically all you want is the files named VTS_01_1.VOB through VTS_01_9.VOB
Here's another way of understanding what is what:
VIDEO_TS.BUP [don't need this]
VIDEO_TS.IFO [don't need this] The first video play item index, usually a copyright notice or a menu
VIDEO_TS.VOB [don't need this] The first video play item
VTS_01_0.BUP [don't need this]
VTS_01_0.VOB Title 01, VOB 0, [don't need this] the menu for this title
*VTS_01_1.VOB Title 01, VOB 1, the video for this title starts here
*VTS_01_2.VOB Title 01, VOB 2, if larger than 1 GB it will be splitted into several vobs
*VTS_01_3.VOB Title 01, VOB 3, and so on...
*VTS_01_4.VOB Title 01, VOB 4, up to 10(0-9) total VOB files if necessary
VTS_02_0.BUP [don't need this]
VTS_02_0.IFO Title 02 index [don't need this], usually for movie extras
VTS_02_0.VOB Title 02, VOB 0 [don't need this], the menu for this title
VTS_02_1.VOB Title 02, VOB 1 [don't need this], the video for this title
VTS_02_2.VOB Title 02, VOB 2 [don't need this], up to 10(0-9) total VOB files if necessary
Btw, with whatever command line program you are using to rip the dvd, there is probably a parameter just to rip only the VOB's for Title 1 and skip the rest in the first place.
As to your handbrake output issue, I haven't converted any DVD's for my TouchPad yet myself so someone else who has can probably chime in on that more quickly.
You might find your answer first in this thread though:
It sound's like people used most of the settings from the ipad preset, but with a few changes.