The Baldwins did indeed have a different control system; otherwise, anything would run
with anything (the early Alco MU system was not compatible with some others; that was
rectified fairly soon). Diesels were MU'd with turbines on the UP; straight electrics
and diesels have been MU'd, I believe.
Mixing and matching was and is done all the time (GE/EMD right now); the GM&O would
run Alco PA's and FA's on passenger trains, and would run the PA's on freights with FA's toward the end of their lives. GM&O RS3's and EMD F3B's ran all over Illinois, MU'd.
But, it was typically more "efficient" in most ways to match the operating characteristics
of the MU's locos, so many roads had a policy of compatibility when possible, and
mixing when necessary. The Southern Railway and/or NS even instituted a policy of
not running 4-axle and 6-axle power together when possible, as the differing dynamics
was less than ideal.
All of which really makes one appreciate what is going on in the photos of a long,
heavy train with two Mikados on the front and two 2-8-0's on the rear being "MU'd"
by skill, touch, sound and whistle. Hot d**n!