I don't think anyone is going to storm out of the meeting over it though. I'm often presented with a paper copy of a presentation which is all in black and white yet the presentation was given in colour and somehow I manage to scrape though. Even when people don't bother putting legends on their graphs (and most don't).
That could be an issue admittedly, if you were hoping to edit the object on the iPad. If you weren't, presuming the objects at least remain correct in relation to each other therefore the effect would be fairly minimal. If it actually displaces parts of the group in the import process then obviously it's a massive pain in the rear.
I generally find automatically generated ToC's need tinkering with anyway so I tend to leave them to the end. So, for me at least, a document I was part way through editing wouldn't have a ToC to mess up.
Yep, this is a problem. Losing content (as oppose to just munging it in some way) surely isn't something two products from the same company using the same file format should do between them.
Jon