Good afternoon, I was reading this thread as I have a similar situation, I do not have MisterFPGA, however, I do have some original consoles, and on many occasions I use them to play natively, basically PS2, PS3, PS4, Atari 2600, MegaDrive/Genesis, (that is all my collection) except my main handheld PSVita where i like to play handheld consoles.
The thing is that I have reached a certain process of automation, which especially began to interest me at the time that LaunchBox began to count the game time, I needed to "launch" somehow the games from LaunchBox for this somehow and thus have those records in my database.
The solution within my reach and that works great for what I'm looking for is the use of run scripts, at first I started with very basic things like a popup window with close button with text like (close this window when you finish your game). I used it as main executable of the game, then I complicated things a bit more, for example with PS4 and PS3, having it connected to the same 4K monitor as the PC, using an application called "controlmyMonitor" that allows execution through parameters in shortcut, I managed to make "controlMyMonitor" change the input source automatically so that when running a PS4 game, automatically launches the PS4 Remote Play, is an application that allows you to play remotely to a PS4, with the same script automatically made the necessary clicks so that the application automatically got into the PS4 remotely, you have to make a series of clicks in the window, I did it with sequential and studied TAB and enter keystrokes. In addition I automatically change the monitor source (with controlMyMonitor), and as I being playing remotely, I can use the same pad that I have connected to the computer, the sound output is also executed by the same means, which saves me having to connect anything to the PS4 except, power and local network, it becomes a very simple method (this same method can be used for PS3 for example with some caveats) for the case of older consoles that I like to play on CRT I basically do the same thing but I have to do the process of turning on the TV and changing the input source manually, sound and controls are native on this case.
Obviously loading the required game is a manual process in this case, but hey, it allows you to complete launchbox statistics and have access to manuals and all the multimedia hosted in Launchbox.
I hope the idea give you a path to run!