To bring conclusion to this thread, and to help out others who may be in similar situations...
The old USB 3 drive I tested everything out on was a 32GB Corsair Flash Voyager Slider (USB 3.0) and it was painstakingly slow. I ordered a 64GB SanDisk Extreme CZ80 (USB 3.0) and it was lightning fast! Incredibly fast!
Straightforward and easy process: Formatted the SanDisk for a Mac, mounted it with a partition table, downloaded and installed El Capitan to it, and it worked great. And while I haven't run any benchmarks, booting and running programs off this SanDisk feels nearly as fast as the internal SSD in the MBP.
Had the SanDisk been too slow, I was prepared to purchase an external SSD over Thunderbolt, but this works out much better. The SanDisk is very portable, and 64GB was more than enough. And now I can boot El Capitan the few times I'll need it, and continue running Sierra 99% of the time on my MBP.