When generating the .qrc files the files from the current project should be taken into account.

Utils::FilePaths Project::files(const NodeMatcher &matcher) const;

You can use Project::AllFiles

auto currentProject = ProjectExplorer::SessionManager::startupProject();
currentProject->files(Project::AllFiles);

This should return all files from the project.

By default, only files from the project should be checked.

Certain files can be always hidden in the table and can be always ignored:
*.qmlproject, .pro, .pri, .qtds. user *

So instead of checking all files by default, only 'project files' should be checked in the table.