As Battuta said, it is never EVER necessary to modify the contents of a vp file.
Let us consider the case under discussion here. You wish to write a table that gives all fighter primaries the "huge" flag (Quite why you'd want to do that is beyond me, but whatever). So, after you created the tbm, the question is where to place it so that the game can see it.
Several solutions are available here, ranked from worst to best:
1. Modify the retail root vp to include your tbm.
This will affect ALL FS2-based mods and games. It's a really bad idea because you messed with data that every modder out there considers to be fixed and static; while the potential for unwanted behaviour is admittedly low in this specific case, neither is this step necessary nor recommended.
2. Put the tbm into <FS2 directory>\data\tables
This is equivalent to 1., except that the retail data remains untouched, making the removal of your custom data a rather straightforward process.
3. Put the tbm into the mediavps VP files
Similar to 1., this involves modifying data that is assumed to be in a certain state by other modders.
4. Put the tbm into <mediavps>\data\tables
Similar to two, except a bit better since you're no longer messing around with the base data directly.
5. Create your own mod folder and mod.ini
This is the recommended way of doing this, since it separates your own custom stuff from the "official" packages and allows you to do further experimentation without having to change official stuff.
It should be noted that using options 1 through 4 also carry the potential of making troubleshooting issues you may run into much more difficult than it has to be, since one of the fundamental steps of troubleshooting is checking whether the retail vp files, mediavps vp files, and their associated directories are in a "known good" state.