For better or worse, there's not really a good way to do it. Kstars/Ekos/INDI doesn't really trigger a meridian flip specifically
, it just does a goto. The good news is we can replicate that.
(From memory, so apologies if any of this is off.)
What is done internally for OnStep is things are compared in location to preferred pier side. Which can be best, west, or east.
What the 'command' for meridian flip does is set the perferred to be east (or west, I've turned myself around I think) then a goto. Best from my recollection prefers to keep it on pointing east if already there (think re-centering target), but if not and it's in the overlap, but close it'll move to pointing west.) So if you set it to pointing west (which should be east) it does the same thing if you issued the meridian flip command. Assuming it's within the limits. (Otherwise neither does anything.)
The limits that you set on things are the auto meridian flip limits in OnStep, and it should be set to ON for the auto meridian flip, with home pause set to off. The Ekos setting is the HA to set it before is Mount/Meridian Flip, and that needs to be set lower than your auto flip limit, if you want kstars to know about/initiate the flip.
Hope that helps. Apologies for it being from memory as I seem to have misplaced the cable for my test board (a mega without anything on it) (Tiny hopefully amusing rant: I can find micro, usb-c, and mini cables, along with nikon camera cables, but not old usb1/2 full size cables. Anyone remember when this was promised as a single universal standard so we wouldn't need serial port converters? Ha! /rant)