Following chewitt's advice, I configured my setup as follows - hopefully anyone with more experience can correct anything that is non-optimal.
System Settings:
Resolution: 1920x1080p
Refresh rate: 60hz
GUI Resolution Limit: 1080 (Comment: I still don't understand why this exists since the Resolution is already limiting the GUI while not limiting the video unless you want it *lower* than the Resolution but I still don't understand the use-case as you can just lower the Resolution)
Player Settings:
Adjust Display Refresh Rate: On Start/Stop (Comment: If you forget to set this, all of your content will be displayed at the resolution & refresh rate in the System Settings)
Sync Playback to Display: OFF (Comment: Off is the default but I am calling it out since it will break audio passthrough and since this is largely a Denon thread, I imagine the vast majority of us want the Denon to process audio)
Lessons learned:
Adjust display refresh rate on Start means that once you stop the content, your GUI will stay in the same resolution as the content you last started which is undesirable if you play 24hz content, now the entire GUI stays at 24hz
Adjust display refresh rate on Always means that if you go into the Kodi GUI (not the OSD but things like your Movies menu) you will get hit with a resolution / refresh rate change back to your System Settings. It is not recommended by Kodi and it is definitely jarring so I don't recommend either.
Adjust display refresh rate on Start/Stop is really best of all worlds IMHO. Your display will get synced to your content's resolution / refresh rate when you start the content. If you browse Kodi menus while your content is playing, it will stay at the same resolution / refresh rate which CAN appear a bit sluggish since you'll probably be around 24hz instead of 60hz but it leagues better than the harsh switch of resolution/refresh rate. Once you stop the content, you'll be back to your System Settings. **This setting could actually bite us Denon owners due to the original bug this thread is about - if you start 4k/60hz content, pause the content, then turn off the Denon, that experience should be effectively the same as having your system settings display and refresh at 4k/60hz since once you turn the Denon back on it will try to display 4k/60hz of the paused content.
You might need to do specific whitelisting depending on your content but I left this off and Kodi switches as needed. If I run into content that fails or behaves weird then I may have to revisit but until then I am leaving unconfigured.
Delay after Change of Refresh Rate: This is one that I am currently playing with to find optimal settings but since there is a delay when the resolution / refresh rate is changed such as when starting 4k/24hz content, this setting will delay the start of the media so it isn't "playing" in the background before your TV/Sound is able to play anything. The delay will be unique to all of our equipment stacks but it is probably something you'll want to play with to find your own best delay.