Are you asking if you can build a “blank” MIDI file template to be used in the BeatBuddy (BB) pedal for use with the Aeros? Or do you want to craft a MIDI song for the BB that has different tempos embedded in a single file?
If the former, I’m unsure of the answer. If the latter, yes you can use time-stretching to set different tempos within the same BB MIDI file (note, this refers to tempos but not time signatures). I think Phil_Flood has created a couple of tutorials for time-stretching using Logic Pro X—the same principles could be applied for use with other DAW (digital audio workstations).
Let us know what you learn and how you applied it to your situation.