I'm a stick user, so take my mouse advice with a train of salt:
Many mouse users use
mpAL, which allows you to use the scroll wheel as a throttle or zoom depending on conditions.
It does not allow delicate control like an physical throttle but frankly you don't really need fine throttle control in Alleg.
Re: multiple controllers
Just because Alleg recognizes one joystick does not mean you can't use multiple controllers...
AHK or Joy2Key can allow you to use several controllers as long as you can map the controls to keys. This does however mean no continuous adjustments (like stick axes).
BTW, I'm planning to buy a cheap dance mat, put it under my feet and use it to thrust back/fwd and boost... more details soon I hope.