> When creating tests, we don't use much of the features, related to grading and still there are other features that we must manually set to the same value every time. We always use deferred feedback, we always have the same settings for giving the student feedback after the test. We always shuffle questions randomly, have time limit and when it's over we want to instruct the system to submit his attempt automatically.
Most (all?) of these can be set to a default and hidden under Site administration ⟩ Plugins ⟩ Activity modules ⟩ Quiz. Set the setting you want to use, then tick the "Advanced" box to have the setting hidden by default. Many other modules are similar.
For the course settings, use Site administration ⟩ Courses ⟩ Course default settings. Those don't have the "advanced" check box to hide them by default. If you wanted to make a patch, you could submit a patch to add "advanced setting" support for courses and for any modules you use which don't already have that feature. See Quiz and other modules which DO already have that to see how it's done.
> If I touch some source it seems that I must say goodbye to this little automation.
This is one reason to submit your patches back, so they will be there in the next version. The review process will also make your patches better. If for some reason you can't get a patch committed, you can always use a local module.