When performing routine maintenance (fluid change) on a 2004 Alison transmission, is it necessary or recommended that the internal filter be changed in addition to the spin-on external filter?

i dont know what the manual says as far as change interval...but me personally i would change any and all filters at the same time.

How many miles?

I just had mine done, (1st time) - external and internal filters, flushed and refilled with synthetic ATF.

2002, 2500HD, 8.1, Crew Cab, Full Box, 55,000 mi.

It made a nice difference. Cost about $330.00

Will do again at 100K +/-