You can probably do this a few ways.
You ask "Will the new versions go into the same folders as the existing masters? Will I be able to pair them (ie in Stacks) with their corresponding masters?" Do you want the answers to be yes to each question? Is this what you want? Assuming so....
My initial thought is that you would export the versions to a folder called Aperture Versions, with subfolders by date or however you wish.
It would make sense to test with a small number of the exported versions. Do a regular Import Photos (not the Aperture Importer tool) and choose Move in the Import dialog. Point the import's destination to the new Pictures/LightroomMasters folder (created by the Aperture Importer tool), and split the import by date. What I think will happen is that the version files will now end up in the same folders as the corresponding masters, and then you'll be able to stack them too.
Does this seem clear? I've not tested it, and I've assumed you selected default options in the Aperture Importer tool (my steps would be different if you set some options). You should back up your LR catalogue before trying it.
This is helpful and makes sense.
Yes, I'd want it to put them in the same folders and have them stacked, since that's probably about as close as I'm going to get to having everything migrate exactly the way it's set up in Aperture.
I'll try it with a small batch. I guess mostly I was just wondering if Lightroom would be able to move them into the existing date folder structure, since the Adobe guide relies on you exporting everything out of Aperture and then importing it into Lightroom (the way I'm doing it basically turns that into a two-step process).
I've also got everything backed up to multiple locations, so this can't go too terribly. I could always revert to my Lightroom Catalog from before Aperture Import and start from scratch.
I'll try it tonight and post back how everything eventually worked out for anyone else interested!