Blueshawk and James, thanks for the comments.
I think I should have been clear about how to test this, and from which repo.
The changes are not in the official Alpha yet. They are in my own branch of OnStep:
github.com/kbahey/OnStep/archive/plate-solve-align.zip
Download this zip, extract it, rename the directory to "OnStep", then copy your Config.h file to that directory, and use the Arduino IDE compile/upload to your OnStep controller.
For KStars and INDI, I am using the versions from Jasem's repositories on Launchpad. I use Ubuntu 16.04.
indi-bin 1.7.3~201805251740~ubuntu16.04.1
kstars-bleeding 6:2.9.6+201805251429~ubuntu16.04.1
Nothing compiled locally is needed for the alignment code within KStars/Ekos/INDI.
Connect KStars to INDI. Go to the INDI panel, then "LX200 OnStep" then "Main Control".
Click on "3 Stars" (Howard says that more alignment may not work on Mega2560/RAMPS).
Sidereal tracking will start.
At this point, note the status in INDI, which will say: "613 Manual Align: Star 1/3", meaning it is ready for the 1st star to align to, out of 3 stars total.
Then in Ekos, go to the Align tab, then click "Mount Model", select "3" for Alignment Points. Then select the stars you want, or let Ekos choose for you, using "Generate".
Then click the triangle to start the alignment. It should be all automated from that point onwards.
You will see 613 change to 623, then to 633. Finally, you should see "Manual Align Completed" when all is done.
I tested it indoors and it seems to do what I intended it to do.
And of course, I would have tested this under the stars if I had a working mount and controller. My project for converting a mount I have to OnStep is still ongoing.
Please test under the stars to see if the Goto is more accurate after you do the above.