The apple 20w charger supports 5v/3A (15w) and 9v/2.2A (20w), like other manufacturers, iPhone also chooses the input while charging, this heating issue comes when the initial thrust i.e., to do 50% in 30 mins or so which means the phone chooses 5v/3A. Once 50-60% charging is done, it switches to 9v/2.2A.
As per my observation, the issue only comes when the input is 3A. In other words, it is not able to manage the heat generated by 3A charging while it is good with 2.2A, I dont know it could be battery getting over-heated or some circuitry.
In any case, I would prefer to do 50% in 5-10 more minutes (with 2.2A) rather than invite other risks with frequent heating upon every charge. To me it doesn't make sense to be 5-10 mins efficient.
If Apple can't fix it, they should either reduce charging amperage or do a replacement. Having said that, I am not sure why it is not with every phone, may be the issue is limited to some specific blocks.