From the symptoms you have described I would be much more suspicious of the mechanism that adjusts the fan speed when in auto mode - presumably it is some kind of small motor/solenoid that alters which resistor the power for the fan goes through. It sounds like the fan speed control itself is fine (works OK in manual mode).
Caveat - my T5 has manual HVAC, so I have no direct experience of the automatic T5 ones. I can't remember reading of this particular problem before, so it seems it is uncommon.
2017 MY18 Golf R 7.5 Wolfsburg wagon (boring white) delivered 21 Sep 2017, 2008 Octavia vRS wagon 2.0 TFSI 6M (bright yellow), 2006 T5 Transporter van 2.5 TDI 6M (gone but not forgotten).
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