VBR (Variable Bit Rate) can be dealt with easily. I remember having to manually seperate the audio and reassemble it in the past, but those days are mostly gone. Make sure you have a current version of vDub, and in most cases it will resolve the issues with VBR automatically, and in just a few seconds.
Worst case scenario, you have to re-encode the entire movie, which can take a hour or so depending on your PC and the size/quality of the file. Just turn off "Direct Stream". In most cases, the program is able to calculate the offset and resolve it with only a few seconds added to the total time. In either case, the root issue is you have two poorly encoded files to begin with. That's why I would stress looking at the file contents or a torrent before getting the movie and try to get one in one piece. If the video is in a rar file, you shouldn't download it. Such compression has a negligible effect on properly encoded video, and no function as a mulit-part archive when delivered via the torrent protocol. The poster is either inexperienced with bit torrent, or they're trying to deliver malware to your computer. Most of the time, with proper downloading habits, this should be a non-issue.
Yes, assembling videos from parts can be an inconvenience, especially if you already have a lot of them. But I maintain that it is better in the long run to work with complete video files. Even with the video named properly and XBMC configured with stacking on, and if MC handles it just as you would expect, there are still issues with multi-part files. However bad assembling video seems (it's not really), I can assure you, hacking apart subtitles to sync is much worse. Also, many of the advanced features of XBMC behave erratically. Bookmarks for are confusing because they still operate based on the file, and not the collection of files.
The best solution is avoidance. Get complete videos to begin with. Very few files are broken up like that anymore. Those that are typically are remnants from the old days of file sharing when people actually put videos on CD (a practice that's fell into antiquity more than 5 years ago for most people, I mean come on, DVD burners are out there for less than $10, who's still ripping VCDs?). Because your probably looking at an old video that's just be re-uploaded, consider this: It was probably encoded with the last generation of codecs. You may find a smaller video of higher quality today than even the best encoding from a few years ago. Even XBMC-Xbox plays the newer codecs smoothly with mplayer, so there's no reason to stick with an arcane format.
Sometimes, there's only one good copy out there and it happens to be parted. This sucks, but it happens. 95% of the time, combining parts to a contiguous file only takes a few seconds.
The 5% of the time that doesn't go smoothly, you may choose to re-encode and spend a hour grinding away on an idle core of your processor.
I just don't view this as a problem with MC. It's a problem with the source material.