Hi Day Tripper,
Glad you've been enjoying the tutorial.
Whether you use Logic's External Instrument plug-in, or its old-school MIDI Instruments really comes down to what trade-offs you're willing to make.
The main reason I use regular MIDI Instruments, is that I prefer to have direct access to the program change parameter and the MIDI mixer channel strip in the Inspector, over having the look and feel of a Software Instrument.
Also, the way that the External Instrument hijacks CC7 and CC10 (which I demonstrate towards the end of video 38 of the tutorial) makes things difficult when working with multi-timbral synths, unless you can dedicate an input of your audio interface to each individual sound.
So there's no right or wrong way, it just comes down to your own personal preference.