Gates

Most people think of the Gates as literal, gate-like structures--this is accurate, to a point, but it isn't the whole truth. Each plane has several Static Gates--alien fixtures that act as conduits between that plane and the Hub. The exact specifics of the Gates vary from plane to plane, but they can always accomodate whatever common vehicles are present. The static Gates connect a specific location in a plane to a Gate in the Terminus. There's no way to hack a static Gate, or otherwise get it to deposit travelers anywhere they're not supposed to go. The process is nearly instantaneous, and as such, traffic through them comprises the bulk of interplanar travel.

However, at the time the Gates first opened, a handful of individuals gained the power to use them without being anywhere near them. These people can jump from any point in the Hub to any point in a plane, or vice-versa. There are some important restrictions on this ability, however. Firstly, the process is somewhat unreliable--intense stress, among other things, tends to make jumping impossible. Secondly, a person with this ability can only travel between the Hub and the other dimensions; traveling from one pocket-dimension to another is impossible.

In other words, this is the explanation for why player-characters can show up in out-of-the-way places in a moment's notice, but be unable to simply warp out in the same manner.

There's one other way to use the Gates. Over the past two years, some parties have gained access to the Ancients' Gate technology; while they've been unable to duplicate it, some of them have discovered actual artifacts that let people traverse planes in the same manner. These artifacts are very hard to come by, and can potentially be stolen by other parties.

Basically, this is an alternate explanation for the phenomenon, explaining how important NPCs and some PCs can travel across dimensions.