Any of the same or similar engines will run just fine in a lash-up. SD70, U boats, etc.. Same engines have the same board, same gear ratio, same wheel diameter. So they will run just fine together. Try to run a consist of say a SD70 and the Challenger and it isn't going to work.
I would encourage Lionel to use the SD70s and ES44s as a standard for future diesel production in terms of Legacy speed and responses so that buyers can build consists of older and newer locomotives without problems. The two SD70s I have run slightly faster than the ES44s, and on curves the faster engines in a consist would push the pivoting pilots to one side until they derailed on a switch. There were only two solutions: keep the SD70s in the lead or use screws to fix the pivoting pilots to prevent their movement. I did the latter. The speed differences were slight, but the adhesion of the traction wheels exaggerated the differences.
As for the U33C, the first generation runs faster than the second, so it will not "run just fine together" with the second generation of U33Cs or the more modern diesels. Steam locomotives are generally OK as single units, but modelers like to build consists of multiple diesels to mimic prototype operations. If RCMC electronics are too big for American Flyer locomotives, then Lionel should standardize performance to ensure compatibility with future products.
(As a side note, Southern Pacific U33C I recently acquired was a surprise. Lionel's marketing department failed to mention or show the SP light package atop the cab, the prototypical L-window for the engineer, or the bell behind the horn. The red emergency light blinks if the user selects the Mars light option after pressing AUX 2 on the handheld remote. The Owner's Manual does not mention this option, and no review I've read discusses it either. Lionel took some extra effort on this model to enhance it but failed to promote it or the other road-specific details on other U33C models. It must have been frustrating for designers to take such pains for accuracy and have them ignored by reviewers and their own marketing department.)