The chip shortage theory would make sense if the 11” was affected too, but it’s not. Last I checked every single 11” configuration is still available for launch week delivery, while not a single 12.9” is. At least in the US. The 12.9” may be more popular this year but not this popular.
Additionally regarding pickups, I don’t think that was available for iPhone 12. I could be wrong, I didn’t care at the time because I wasn’t upgrading, but to me the lack of in-store pickup has to do more with Covid than the device shortage.