Generic 3-star alignment is used to get an overall correction over the whole hemisphere. Because the corrections occur in sky patches, you may still get incorrect precision on particular positions. Atmosphere refraction is always a problem, and will be in the case of the eclipse as the altitude is quite low. You should probably use three or more sync stars close to the target area.
If the offline version times out, it means it is not looking at the right area. You specify a maximum angle for the search, and the time needed for a match increases non linearly as the engine goes away from the expected position. First, when testing don't align near the pole because of the lower precision in the coordinate/gear relation. Second, use the most narrow search angle your setup allows, this will make the engine fail quickly when something is wrong with the orientation of the mount: if you expect your mount to point within 5 degrees of the target in any direction without correction, use that value. Third, remove as many index files as you can: you want the engine to only search catalogs matching your optical setup. Fourth, adjust the timeout to your configuration and computer capabilities: while testing, the engine should fail to find a match in the catalogs, not abort the search because it's long. The online engine searches the whole sky for a match to answer your request, you only need to adjust the centering of a target that is already roughly there.
That's only because the mount was pointing close to the target. Maybe having too many sync points in an sky patch is causing issues with the interpolation? Maybe a better way would be to sync evenly spaced locations, then never do a target align again? I didn't touch the subject, I don't have a fixed setup.
I am not, unfortunately, and I have doubts this feature can ever be robust enough. There's a branch on my github with code to automate guide star selection, calibration and start/stop, plus a preliminary PHD2 network interface. But this bases on blind navigation scenarii, and I felt the Ekos scheduler needed more love for the time being
-Eric