[Wolves] what the difference between install with apt-get and downloading binary install

[Mark Croft Redditch Linux Mint]

i have come from windows background so i do not fully understand how
linux mint/ubuntu installs software looks a lot more secure and
professional then some windows installer i have seen in the past.

i am install unetbootin (cos having problems making linux mint usb boot pen.)

http://unetbootin.github.io/linux_download.html

shows to methods one with add new repository which is what i do most
of the time when i can't find application in package manager.
was just wondering if the binary version would be doing the repository
and apt-get all wrapped up in single executable program? I guess linux
have a number of different ways for programmers to install
software/apps and they can ignore all the good practice such as
happens in windows world a lot.

is there an application that will scan linux distro and create a
script of all the applications installed , sort of method of doing a
fresh install. I guess would have to backup all the settings it knows
about (i guess some apps create there own settings files and break the
rules - have done it in the past but was restricted in how much of the
windows i could use inside autocad long time ago with windows NT
3.5/4)