I don't think he's confused about how it works, he's just saying that it's nonsensical that the bonus is a fixed amount instead of a percentage, which makes it only really useful/rewarding on lower priced passes. I had the same thought when going over all the various bonuses and gifts and whatnot as the AC ecosystem is relatively new to me as well.
As an example using an Eastern Canada to Asia pass vs Ontario mining pass, both 8 credit LT passes:
8x YYZ-NRT gets you 63,912 SQM, the 50K bonus of 1250SQM amounts to a rounding error and isn't likely to affect anyone's decision as to whether to buy a nearly $20,000 pass
8x YYZ-YQT gets you 5,664 SQM, the 50K bonus amounts to a 22% bonus, which isn't bad at all and would be worth taking in to account when deciding whether to buy the pass or not.
Pretty much everywhere else in the program, percentage bonuses are used as they make way more sense. (At least to me and Aphrican!)