"Preferred" is hard to answer, since it's a preference. Everyone has their own. Mine is the inline reactor for a couple different reasons.
The large diameter of the reactor section will slow down the flow inside that particular section, which is what you need to keep the air inside that section. If you didn't make that section larger to slow the flow down, it wouldn't work, it would just blow the co2 bubbles into the tank. Slowing the flow in that section does not affect your overall rate. After the water goes back into the normal sized return, the flow is pushed back up to it's original rate (or pretty close to it).
What can affect the flow rate when you add stuff to your plumbing like that is the number and the degree of the bends. Those will generally be minimal though, unless you have a real fetish for a lot of right angles to get you connected.