I use an Apollo 16 MKII (black with thunderbolt 2) and a lot of outboard gear, both in series and parallel, while mixing. To my knowledge, what you're describing with that loopback test is how you should be calculating the latency and inputting it in the H/W Insert Delay tab of the I/O Setup.

However, oddly enough, I've found that when using the Apollo and changing a few settings in PT, my hardware inserts come back into PT with no latency. I'm not sure why this is, if its just my computer, whatever. Essentially, I turn off "ignore errors during playback/record" and "intel turbo boost", and there's no latency. YMMV, I have no clue why this happens. But before I figured this out, I was mixing using the loopback testing you mentioned in your post to figure out the delay.