It doesn't make sense to you because probably you only have in mind the people who payed for their MadeSafeCoins using BTC... run the maths for those that payed using MSC... that should clear up the situation for you pretty well...
The MSC sale was problematic is so many ways. If 1/2 of all safecoins were purchased at a 50% discount, then the actual average purchase price is at 3151 satoshis per safecoin. In fact, the current market price is a bit over that price now.
I would not do a crowdsale with mastercoin if the requirements was that MSC holders would get a 50% discount. Well, let's just hope this is a temporary condition that safecoin is dependent on MSC.