Sites and games establish their own currencies to help distance you from your intuitions and inhibitions about money.
A small purpose is to get you to make fewer, larger purchases. You might flinch from putting down $0.99 every time you want to get a pack of imaginary cards. Buying five of them is five separate pain points. Getting you to buy 250 gems for $5 is one pain point, and then it is a lot less painful to buy 5 packs of cards for 49 gems each.
Once your players have converted their real world currency into your game currency, they are committed. It is not hitting their wallet anymore, and it is not as though they can spend those gems on anything outside your game. Why not pick up that shiny mount or xp booster? And might as well round out that shopping cart with something to use up the last few gems, no point in wasting them.
Soaking up those last gems at the edges is the minor gain, a few bonus nickels and dimes. Because you got as close to zero as you could, and now there is a new shiny mount that you do not have enough to get. Maybe you should make another purchase? Or make all the purchase amounts add up badly so zeroing out is not reasonably possible. The $25 gem pack comes with 250 bonus gems, taking you to 2750, but most (good) things are in units of 495. Maybe you should buy another $25 and round that up?
The main purpose is to put psychological distance between you and your spending. It is not just that five small $1 flinches are worse for sales than a $5 flinch, but that a $5 flinch is worse than a 250 gem flinch. You have decades of experience with money but very little with gems. Setting your emotions aside, you need to do arithmetic to figure out how gems relate to dollars, the horror. And “100 gems” looks closer to $1.00 than $2.00, doesn’t it?
You can see sites and games combine these. I have played Spellstone on Kongregate, where the main currency is gold and the RMT currency is gems, but Kongregate has its own currency of Kreds, which you buy with a credit card instead of physical bills. Your hours at the workplace are way over there, behind your paycheck behind your credit card behind the kreds purchase behind the gems purchase behind the gold conversion. And didn’t they give you some gems and a few kreds? This might be a free pack of imaginary cards! I saw Spellstone on mobile, where there are some actual dollar amounts, and I got sticker shock in a way that the prices in kreds never caused.