OK, before I try and create an AHK file that ALWAYS runs in Windows to close Future Pinball the way I want and change a few of the non-configurable keys to work with my X-Arcade tankstick, I thought I'd try my hand at creating an AHK file for each table the way I've done for individual Roms for emulators such as Demul and Supermodel 3.
The following AHK code works perfectly inside and outside of MALA. The main advantage is that I can use the 2 & 4 keys together to exit AND I can map a bunch of non-configurable buttons to my X-Arcade controller. The downside is that I have to create an AHK file for each and every table I want to list and play in Mala. I've collected quite few.

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SetWorkingDir, C:\Arcade\Future Pinball\
#SingleInstance force
Run, "Future Pinball.exe" /open "C:\Arcade\Future Pinball\Tables\Superman.fpt" /play /exit
WinWait, (c)
WinWait, BSP
WinWait, Software
Sleep 500
WinActivate, ahk_class FuturePinballOpenGL
WinWaitClose, BSP
Ctrl::F1 ;Full Table View 1
LAlt::F2 ;Full Table View 2
Space::F3 ;Scrolling View 1
LShift::F4 ;Scrolling View 2
z::F5 ; Low Angle View 1
x::F6 ; Low Angle View 2
c::F7 ; Fixed View
5::F8 ; Special Views including Apron View
[::F11 ; Free Camera View
r::Numpad8 ;To set alternate Nudge UP control. Numpad8=Nudge Up in FP preferences.
Numpad4::d ;To set alternate Nudge Right control. D=Nudge Right in FP preferences.
g::Numpad6 ;To set alternate Nudge Left control. Numpad6=Nudge Left in FP preferences.
Numpad2::f ;To set alternate Pull control. Numpad2=Pull in FP preferences.
a::Tab
s::Send, {Pause} ;To Pause and/or view high score table
w::PgUp ; To set Music Volume Up
]::PgDn ; To set Music Volume Down
e::Home ; To set Sound Volume Up
6::End ; To set sound Volume Down
~2 & ~4::
Send, {ESC}
Process, Close, Future Pinball.exe
ExitAPP
return
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Of course for the above script to work, the executable under the OtherEmuConfig tab/Basics must be set to "explorer.exe"
Rom path points to a folder that holds the AHK script(s). Rom Extension is ahk. Command line is "%path%\%rom%.%.ext%".
I've also made an attempt at creating a "Table Launcher" script that would be global for all "roms" or tables passed from Mala to my AHK script compiled as an .exe file. It's my own Mala wrapper I suppose. It's NOT working, but I think it's close...maybe. If I can't get this to work and still only want one AHK file to control Future Pinball settings, I'll go with BadMouth's suggestion. I may have to post this in software to see if I can get some guidance. I point Mala to the my "TableLauncher.exe" file. Rom Path goes to my Tables folder, Rom extension is "fpt". Execution I think is still "%path%\%rom%.%.ext%". I'm just not sure how to pass and use the name of the table as the rom name in the script to use it to launch any table. Below is my code:
SetWorkingDir, C:\Arcade\Future Pinball\
#SingleInstance force
Table=%Rom%.fpt
Run, "Future Pinball.exe" /open "C:\Arcade\Future Pinball\Tables\%Table% /play /exit
WinWait, (c)
WinWait, BSP
WinWait, Software
Sleep 500
WinActivate, ahk_class FuturePinballOpenGL
WinWaitClose, BSP
Ctrl::F1 ;Full Table View 1
LAlt::F2 ;Full Table View 2
Space::F3 ;Scrolling View 1
LShift::F4 ;Scrolling View 2
z::F5 ; Low Angle View 1
x::F6 ; Low Angle View 2
c::F7 ; Fixed View
5::F8 ; Special Views including Apron View
[::F11 ; Free Camera View
r::Numpad8 ;To set alternate Nudge UP control. Numpad8=Nudge Up in FP preferences.
Numpad4::d ;To set alternate Nudge Right control. D=Nudge Right in FP preferences.
g::Numpad6 ;To set alternate Nudge Left control. Numpad6=Nudge Left in FP preferences.
Numpad2::f ;To set alternate Pull control. Numpad2=Pull in FP preferences.
a::Tab
s::Pause ;To Pause and/or view high score table
w::PgUp ; To set Music Volume Up
]::PgDn ; To set Music Volume Down
e::Home ; To set Sound Volume Up
6::End ; To set sound Volume Down
~2 & ~4::
Send, {ESC}
Process, Close, Future Pinball.exe
ExitAPP
return