JAL Award Redemption / Stop-Over Rules

Hi,

I'm looking to book a round trip award using JAL Miles for travel on Bangkok Airways. My itinerary would be as follows

Leg 1: BKK-REP
Leg 2: REP-USM (Via BKK, although it as marketed as a direct flight with one flight number
Leg 3: USM-BKK

Can this be booked as one roundtrip itinerary, qualifying for the 5,000 mile price (under 1,000 miles)

I ask as I am am a bit confused on JAL's stopover rules, specifically this one:

Since technically I am starting in, ending in, and transiting through BKK (although on a direct flight) I am wondering if this will be allowed.

Also, does JL see the same Bangkok airways availability that expertflyer does?

Thoughts?