As roommates, they were always having fun, and so by the time they actually did get together late in the show’s run, there wasn’t THAT much that was different.
They continued to be friends, both then and even after they decided their relationship wouldn’t work (because of the friendship, which is dumb).
Even though Rachel’s occasionally high-maintenance lifestyle didn’t firmly mesh with Joey’s sandwich-guzzling goofiness.
To try and sum up this argument somehow seems more tasking than summing up ten seasons of Friends, but a lot of what it boils down to is that from the very beginning, Joey and Rachel actually were friends with each other, and they almost always enjoyed their time together, regardless of what they were doing.