Actually I do have a Logitech K400r Bluetooth keyboard. However, I don't have Setpoint running. It is not visible in the Task Manager, or Services. I am just using the Unified device driver and whatever gets started with that. In fact, Setpoint is installed, but it doesn't run. It was always a rubbish bit of software, and it just crashes if I try to run it. That may be contributing to my observations. Or maybe just by having the K400r installed and operational I get different results. One other possible difference is that I run my HTPC using a limited Windows Account, rather than an Administrator Account. The HTPC account doesn't have access to change system settings of course, which could make a difference.
Whether the MC User Interface is running or not, pressing the Play button on the K400r starts playback of audio or video in MC. The Play/Pause, Mute and Unmute buttons all work, always. I guess that is the same as your observation, in that when Setpoint isn't running, the K400r behaves, to some degree, as a remote.
But at the same time, with Setpoint not running, my Logitech 880 remote control running as an MCE remote never starts playback if the MC User Interface is closed, and just the MC Server is running, as I described above.
I didn't test what happens when the MC Server also isn't running.
It would be good if there was a way to watch the command processing of IR and Bluetooth commands within Windows, to see which programs handle them. I haven't looked for a tool that would allow that, so maybe there is something available. (Well, I know there is for IR. Not sure for Bluetooth.)
I wonder if your case is just Windows receiving the IR and sending it to the default program, rather than the currently active program. If the MC Server received the signal, no doubt it would play the currently selected media. Maybe Windows 10 changed the way IR commands are handled, in which case there might be a setting for it. As per my signature, I'm still running Windows 7.