That setup works just fine if you really want the new ships to override certain ships every time that FSPort directory is enabled, which is in this case desireable I would think. It's a perfectly good way to do things if there's no need to easily revert to "official" FSPort behaviour. Multimod offers that, if it's required. Putting the VP into the directory works just fine - in most cases anyway. If there are textures and/or models with same name in multiple VP's in same mod directory, the I guess some of the overriding rules in the code will decide which one is used...
Putting individual model, texture, table and other files into FSPort\data\models etc directories will always work and files that are put there will always override the files with same namy that might be in the VP archives in the same mod directory. That's the only advantage over VP files
that individual files have IMHO. VP files have every other advantage to their side. They are easier to distribute, generally way easier to install and easier to manage than craploads of individual effects, textures and model files in mod/data directories.
ShivanSPS' and Turey's downloads work just fine. I'm sure they have tested the directory structures before distributing their work. I only have experience about Shivan's download - I DL'ed it because my CD's were 700 km north - and I haven't noticed any problems at all. Besides, both of them are meant for people who just want to start playing with latest graphics and stuff, and haven't really familiarized them with how FSOpen directory structure works. It saves confusion and works fine, so it's a good solution.
I'm just saying that there are many ways to get things working and as long as you know what you do (and do what you know) it doesn't matter how you do it. It's greatly down to personal preference how you want to get certain ship to work - by integrating it to previous mod folder (like FSPort) or running it from separate mod folder with multimod command line, both work. In some cases, other one works better than the other. But as long as you find a way that works, everything is okay. It's just that some ways of getting stuff to work are better than others. Like, for example, you should almost never install anything extra in main data folder...
I personally prefer keeping "official" releases such as FSPort directory as clean as possible, and I put possible modifications that I want to run with it into separate mod folder. Then I just run both mod folders simultaneously. If I run into problems, it's way easier to do trouble shooting. Turn the other mod directory off - if the basic FSPort works, I know that the problem is somewhere in my alterations.
Fore example, it would be possible to put, for example, Apollo_HTL.vp and Valkyrie_CPR_high.vp into another folder named, for example, FSPort_newShips - directory, and then just run a command line -mod FSPort,FSPort_newShips or something like that. But as I said, putting them inside the FSPort dir works too, as long as you remember that they are there.