how is the fluid pick up point extended if the standard filter is used
Ideally you use a filter that has a longer neck that places the filter to the bottom of the pan like immortality said, otherwise the pickup point just remains the same. The other thing about trans filters is that they usually sit directly on (or quite close to which at least keeps them captive) the pan, so keeping them in place or stopping them falling off if you use a standard filter with an extended pan may be an issue.
While it's really not ideal, having an extended filter isn't 100% necessary and you can probably get away with using the regular one on most transmissions, at least for regular driving or towing or something (although it's still probably not a good idea) - you might do this if there's no deep pan factory option (so no OEM style deep filter) or aftermarket extended filters just aren't commonly available because you're using an uncommon trans or made your own extended pan e.g. uncommon height or strange shape to swap the trans into something else. In this case you'd try to get/make a baffled pan that would also have some raised sections to support the filter that don't interfere with fluid intake.
The other big advantage which I'd do it for just on this alone is that most extended pans come with a drain plug.