Expedia should let you do MIA-MGA-SAL on TACA 514 as two separate flights, if you select the "build your own itinerary" option.

Yes, it costs more, but if you book it as a one-stop, you'll only have one boarding pass, and I can see LatinPass arguing that it should only count as one flight. I'm willing to spend a little extra to avoid that hassle.