What does the scene where Walter and Jesse meet in a cafe mean?

The importance of the scene in relation to El Camino is that it's Jesse finding closure with his old (Breaking Bad) life. It's not just Walt, we also see memories of Mike and Jane.

The scene very much highlights a part of Walt's character that defined Jesse's interaction with him, in a way that Jesse now retroactively think he should've seen the red flags.

There are a few small things here: Walt is giving unsollicited fatherly advice, Walt assumes Jesse didn't graduate (it reveals how Walt thinks about Jesse), Walt is generally meddlesome (telling Jesse what to do/achieve) though he intends well. But the most important element here is found in the following quote:

You're really lucky, you know that? You didn't have to wait your whole life to do something special.

It's not the resentment that's the big issue here (though it does contribute), but rather that Walt is clearly in love with what they are doing. Walt's love for his activities is what will eventually lead to his downfall and that of everyone around him, leading to Jesse's life in a cage and subsequent life on the run.

You can even see it in Jesse's response to that quote. He's initially dumbstruck, clearly trying to figure out if Walt meant what he said. Once Jesse realizes that Walt didn't misspeak, he bows his head in avoidance, which implies he disagrees but is not willing to get into it.

While it is only in later seasons that we find out that Walt is in love with building an empire as opposed to making meth or making money; the point of the scene is that Jesse is reminding himself that he should've seen the red flags way back at the diner. He somewhat did notice it then, but he dismissed it and continued working with Walt.

Jesse was seen wearing a cap that Skinny gave him. Is that scene linked to his present?

As @Charles already mentioned, it's not Skinny Pete's cap (which is full black with a white logo). It's Jesse's own cap. It just happens to somewhat resemble it.

According to THR:

The Walter White scene takes place within the space of season two's "4 Days Out", one of the most celebrated episodes in the Breaking Bad pantheon, in which Walt and Jesse's RV breaks down in the middle of the desert; it's one of their closest bonding points in the show, hence Walt's less-threatening-than-usual demeanor in the restaurant.

However, Aaron Paul looks at it differently:

Although the diner sequence portrays a tamer version of the mass-murdering Heisenberg seen later in the show, Paul clarified the scene still doesn’t signify Jesse’s feelings towards his former mentor have softened.

“He still despises the man,” he said. “Walt completely turned Jesse upside down, from the moment he met him and just shook his life to its core. Because of Walt Jesse became a murderer. Because of Walt, the people around him started dying. I think he feels very let down by the man. Very disappointed. And just angry.”

Paul added: “That flashback with Walt was such a beautiful scene and so eye-opening. It really showed what Walt was all about. When he says to Jesse ‘you’re so lucky it didn’t take your entire life to do something special’ and he’s talking about making meth – that’s pretty terrible!”