This is how this works because it doesn't work the same for all. If a film mentions a character belonging to another company of any kind, it's full and legal because in the credits they are giving proper credit to the company that owns said character and it's free advertising. Most movie studios do not like to give away free press, so they try and strike a deal for product placement even in mentions of the character but usually if it's dialogue based and one second's worth of time, it's usually passed. If I mention The Thing it's usually just shrugged, if I walk around in a Thing t-shirt, then the studio will go to Disney/Marvel and say "Give me XX amount of $$ because we are advertising your character" if they don't usually I won't be wearing that shirt. Within your own studio like the DC characters though it's moot. This is kind of why on TV if they are using a Coke can, that everyone knows is a Coke can but Coke didn't pay up the advertising fees its says "Soda" or "Cola" even in the Coke script.
Now with Marvel because they signed over complete perpetual rights to those characters in regards to film likenesses and content, these characters don't exist within the same universe. Basically in Marvel's film universe there is no Spider-Man or Wolverine. This isn't like when Batman mentions Metropolis or if Superman were to mention a masked vigiliante because those rights weren't outsourced. So if Captain America were to mention how they have to go to Reed Richards for something even if he didn't appear, it's a film reference to a character owned perpetually (meaning it never expires) by 20th Century Fox. Marvel Studios would have to pay Fox because Fox could make the case that it could damage their own projects in place especially if they were doing a period piece for example like First Class and something eluded to within a Marvel film said otherwise. Fox can sue (and has) for just the eluding to the idea of Mutants in a Marvel production on Television and won because even the idea of mutants was signed over by Marvel.
When Marvel made those arrangements they were in bankruptcy and unsure if the doors would even remain open passed that point. They literally sweethearted the deals as rich as possible and essentially screwed themselves with Fox, Sony and Universal. Disney lawyers have been working since they purchased Marvel to try and get them out of those deals but they are pretty straightforward. Even introducing or using a character that is a "knock-off" of an owned character is infringement.
You'd get a better shot of them using Jessica Drew Spider-Woman and having her fill the void then actually ever seeing them using a Spider-Man similarity unless the scenarios go into place where both companies sat at a negotiations table and hashed out some sort of agreement.
Essentially the fact that Marvel owns all of those characters doesn't mean crap as far as the film world is concerned because of the original contracts.
