It's a relic from the old days when champions were cheaper and there wasn't so much to spend IP on.
It's not really there for any reason other than "it has always been like that".
I'll quote quote myself from the other thread about this topic:
[{quoted}](name=Nameless Voice,realm=EUW,application-id=3ErqAdtq,discussion-id=KgA4jBHA,comment-id=0003,timestamp=2017-02-10T11:11:59.429+0000)
I think that they should just give everyone 20 free rune pages and free runes.
(And give everyone the full 30 slots from level 1; same for masteries.)
When runes first came out, they were something for players to aspire to, to give you something to spend your IP on, and to encourage players to spend RP on champions in order to save IP for runes.
League's economy has changed. Riot make their money mostly from skins now, and new champions. The prices of new champions have gone up a lot from the days when we had 1350 IP champions released, which further encourages players to buy them with RP.
There's no longer any reason for runes and rune pages to be so expensive. IP as a currency has been greatly devalued because all new content costs so much, making it prohibitively expensive for new players.
I think the potential money that they would lose (from people having a little more IP to spend on champions that they might otherwise buy with RP) would be offset by making League much less difficult for new players to get into.