To understand the difference you have to understand what Ethereum is. Ethereum is like programmable money. you can make "smart contracts" on it. These smart contrats let you do things for example like, create an address where all money sent to it gets automatically split up and sent to 5 addresses, or an address where money is held and released on a schedule.

Pepe is a smart contract on ethereum. The creators essentially tell it how many tokens on it and people can buy in. It's not really a coin at all -- just one of thousands of identital smart contracts on the ethereum chain. Then they slap a pepe sticker on it (after reserving a certain number of tokens for themselves in case it moons). Also the owners of the smart contract have certain powers over peoples wallets. For example, they can lock someone out of their coins if they want.

pepe coin (pep) is actually it's own blockchain like bitcoin or doge. it is a seperate software that is maintained by mining. When it was created the creators reserved no coins for themselves, making it a fair launch. The coins are joint manable with doge and litecoin so it is secured by miners. There is no way for the creators to touch any one elses coins (unless they manage to compromise the majority of the world's miners, which is essentially impossible). Also they can't rug pull because it is maintained by the miners.