Don't forget that when you polar align, you're pointing near the celestial pole by definition, and there, RA visually corresponds to a rotation of your scope around its optical axis. You could be 12h00 shifted in RA at the pole, Polaris will still be in your FOV, simply it will be on the wrong side of the celestial pole. Polaris being only 45 arc minutes from the pole, you should be very precise when you make your alignment (depends on the magnification of your polar scope). Your 20 minutes error is only a 5 degrees error **in rotation** of Polaris around the pole. Maybe half the diameter of Polaris itself as you see it through the polar scope (just an estimate). And if you simply spent 5 minutes between the time you set the RA angle of Polaris in your polarscope and the time you finish your alignment, you're 5 minutes away.
Not sure where your 20 minutes error comes from, as you did not find the AlignData file, that may be a plate solve/sync near the pole. Here too depending on the resolution of your imager and the quad star the astrometry solver finds in your image, you may get high error in RA when you sync near the celestial pole.
Anyway the problem with the meridian flip not occurring is a software issue, it seems that INDI/Ekos/client devs have to discuss this point and decide the correct way to go for mount drivers which can sync.
In your situation you may simply set a flip HA 1.00 hour past the meridian, just check your setup allows for that (it depends on the declination of your target though, your latitude, your pier...). That way you may live with a 20 minutes alignment error, the meridian flip will occur 1h00 past the celestial meridian.

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