While I would still like to see custom mapping for hardware keyboards, I have a temporary workaround that might be easier to implement in the short run.
I have Smart Keyboard Pro set to "Advanced settings -> Ignore hard keyboard." This makes the soft keyboard come up when the hard keyboard is out, but does not "ignore" the hard keyboard. Both work simultaneously.
So I switch the soft keyboard to the Alts board, and then type letters on the hard keyboard and alts/numbers on the soft keyboard. The only trouble is, the alts keyboard will often switch back to the letters while I'm composing a message, so I have to switch back to alts/numbers every time I need to use one.
Would it be possible to add an option where the soft keyboard always stays locked on alts/numbers when using with the "ignore hard keyboard" option?