The problem is that they're using it for encryption.
Anyway, I have seen sites where it was used as a security measure. Or so the authors thought I guess. Storing login password in url parameter? Seems safe if it is encoded.. But it was years ago.
Both ; and = are perfectly valid.
There's nothing wrong w/ base64 encoding; however, one needs to apply it to the correct context like applying it to: hashes, avoid text collision/escaping chars, or just embedding plain old non-sensitive binary data in text.
It's very easy to Google and see tons of sites using it. Many sites using it got serous security flaws.