Main reason is, they don't want people to send a friend say, 10-20 mystery skins a day and vice versa, or in the case of some people, they will make an alternate account, and send their main account mystery gifts to get cheaper skins and such.
For 80% of skins, they are more expensive on their own than getting them as a mystery gift. Riot doesn't want someone being gifted, say, Pulsefire Ez, and so on for a fraction of what it actually costs.
While we the player would like that, Riot wants people spending their own money and rp full price.
I see where they are coming from, even if I wouldn't mind having a cheaper alternative.
While they are getting money, they aren't actually getting the same amount, so they aren't still getting their money out of the skins.
975 for Imperial Lux as an example
490 for a mystery skin
That is near half. They don't want that to become a norm. Most of the skins are 975 and above, some of the cheaper ones are still more at 520.
If you were in their shoes, you'd rather people spend the extra cash to get even the 520 than the 490.