As far as I can see they are the same. I just asked my Mexican friend and he said they were the same too. I think in literary contexts 'comía' or 'hacía' etc would be preferred instead of 'estaba comiendo' or 'estaba hciendo', because they're more precise, or elegant.
What is more difficult is that the imperfect (past continuous) is used in contexts where an English speaker would use the preterite, for example, 'en aquel tiempo tenía 5 años' = I was 5 at that time.