So, I think I solved my problem by using the DBUS interface into the Ekos Align module to set the Target Coords.

Roughly:

...
bus = dbus.SessionBus()
align_object = bus.get_object("org.kde.kstars", # Connection name
                                "/KStars/Ekos/Align" # Object's path
                                )
...
# after slewing
...
align_iface.setTargetCoords(target_RA_value, target_DEC_value)


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