I suspect that your supposition (i.e., that the reason Apple has not incorporated “rapid charging” into its iPhones yet is the problems it can cause lithium ion batteries) is correct and that Apple is being appropriately cautious.
It may be that Apple is taking a very rational step-by-step approach to adopting rapid charging only when they have ALL their software & hardware ducks in order to accomplish it successfully. We bought a new iPad Pro last year when they first came out — it did not have rapid charging. It wasn’t until earlier this year (May 2016?) that Apple came out with a new 29W USB-C Power Adapter & a companion USB-C to Lightning Cable for the iPad Pro. Using the new 29W USB-C adapter & lightning cable with our iPad Pro yields VERY rapid & impressionable charging. I guess that Apple held off on offering this capability until THEY were happy with it -— with the result that MY family is also very happy with it. And our house has not gone up into flames so it was worth the wait until Apple had a superb & safe product to release.
It is faster, but it still doesn't do a super-fast charge like the Android approach where they can get a 60% charge in 15 minutes, then the next 40% in another hour or so. That's too much stress on any Lithium Ion battery. These batteries do swell a bit when the charge, especially when they get hot. Do that too many times and there will be internal changes.
Even with my new iPhone 7 plus, the first time I charged it, it got hotter than I felt comfortable with. After the latest iOS update, it doesn't any more and it charges faster than it did before. Something in the software update manages the charging better.
My iPad Pro (12.9") doesn't ever overheat on charging.