My 2016 EX has been charging and running perfectly fine on an AGM battery for 3 years now. I got tired of having to replace the feeble 51R batteries every 2 1/2 to 3 years, so I upgraded to the larger Group 47 size. Just had to replace the battery tray with one from a Honda Odyssey.
I've also installed an AGM battery in my wife's Aunt's 2014 Lexus. I've never heard of this issue that you're referring to. An AGM battery should charge and perform fine in any 12 volt automotive application.
Upgrading to a group 47 with lead acid may have yielded the same results, not sure.
Here is a the NOCO battery charger manual page, automobiles are not able to switch modes, to my knowledge currently.
Although, the TSBs I see mostly say people go cheaper and replace there AGM with FLA and that is where the problem lies, so you may be just fine.
If its working for you all, great, but for the extra cost and if the battery last the same, then I don't see the point.