- If you register for Part 107, you may also fly that drone under section 44809. Registering this way requires you to provide the drone's serial number, and you get a number that is good for that drone only. So if you have ten drones, you'll have to get ten registration numbers.
- Registering for Section 44809 gives you one number which you may use on as many drones as you own. It only allows you to fly them under section 44809, even if you hold a Part 107 license. So you're restricted to flying under the "strictly for recreational purposes" limitation (along with all the other limitations) of section 44809.
When you register under Part 107, you don't have to provide a Part 107 certificate number, and you could actually register a drone that way before you passed the Part 107 test (or maybe after you received a temporary certificate but before you have your permanent certificate in hand). That might save you the cost of re-registering the drone, if you were planning on getting a Part 107 license and registering the drone that way soon anyway.
If you have two drones that you consider "professional", and five drones that you consider "toys", you might decide to register the professional drones under Part 107, and then register the toy drones under section 44809. This wouldn't allow you to perform commercial flights with your toy drones, but it would save you a little bit of money that it would cost to individually register each drone under Part 107. It's your decision; just make sure that every drone you want to fly under Part 107 is registered individually with a Part 107 registration number.