In https://issues.jenkins-ci.org/browse/JENKINS-20327 you said that this issue is not a core problem but a problem of the job configuration slicing plugin.
To clarify, I meant that Marco's comment did not refer to the issue the other report was about (moving the goal posts after a change was committed isn't useful); not necessarily that it's a bug in JCS.
Why does the configuration slicing plugin lists all the modules of a job at all?
This should have been fixed in 1.37.1, released over a year ago. Looks like
JENKINS-18455 was reopened because of this, and it's tracked there.
The problem is that the plugin sends huge forms by design (that's how the UI works) if there are many projects, and current Winstone-Jetty doesn't like that. If that is what this report is about, then please reopen (and clarify that in the issue description). A redesigned form may help here.
But since the plugin has no control over embedded Winstone-Jetty, it cannot increase the limit on its own. (And FWIW, that is already being discussed in https://github.com/jenkinsci/winstone/pull/20 so maybe this is soon obsolete anyway)
To just get rid of the problem (one instance's DoS protection breaks another instance's config forms), you can set the System property as described in the other issue reports.