These are great questions.
A cloned template is independent of the parent. What you do in one will
not affect the other.
A corrupted template will not affect the parent. That’s why many users
will clone the basic (e.g) debian-10, and install software and
configuration in to the clone.
If anything goes wrong you can always step back to the original, clone
it again, and try again.
qubes inherit /home/user from /etc/skel in the template, not from
/home/user in the template. This only works if you create a qube - it
wont work if the qube already exists and you change to use a new
template.
So if you want folders to appear in the home directory you need to
create them in /etc/skel in the template, then create the qube.
If you mean that some apps don’t seem to appear in the qube, look
here for some tips.
It may be that the app is there but shortcuts have not been created.