I don't see that as silly. What character would most kids or parents buy if they could only afford one Voyager toy - The main character (Optimus), or a character that is about the 5th or 6th most featured character (Bulkhead)?
Serious collectors like us may buy both, or critically evaluate both before buying either, but we make up like 10% of those purchases... leaving up to 90% of Voyager purchases to kids & parents who only buy one toy.
If Hasbro had equal case ratios for toys that are not equally featured on the cartoon, they risk shelf-warming the less popular character toys. I don't think they just randomly generate those ratios - they'd do some polling first I'd imagine, or at least order the importance of the show characters (and non-show characters) and estimate the best ratio possible to minimise shelf-warming.
(and the problem with the larger toy sizes is that there are less figures to a case, so less room to move on ratios - 3:1 may seem over-balanced, but 2:2 would be out of the question for two mismatched characters)