Before going through this i suggest to cover up this HERE to understand exactly to the core .

As earlier we been through, what is software ,OS,and ANDROID. I will put in nutshell

Now the things which makes you scratch your scalp are STOCK? ROOTED? let's go through them, before that we will glance on commercialization of software.
Manufacturers and Developers of
a software give access to only certain files of software for modification,customization is a popular illustration.They hide the other part in order to overcome messy modification you would do without knowledge if  accessed, as they  should go through this messiness in order to give you  best “costumer support”.So if they cut of the access to other part ,which is usually very sensitive,they are at least confirmed that the sensitive part or core part is okay, whatever the problem is; it is in the accessed part thus they could do asap and give best “customer support”.
Same applies to ANDROID ,the developers encrypt certain core files of operating system and allow access to other part for costumer customization.The operating system which has encryption for core file is called STOCK, unmodified,rootless OS and if this access is granted by developers or you yourself tweaked a way to access this part then such OS is called ROOTED,modified OS


ROOTLESS ANDROID SCHEMATICS



ROOTED ANDROID SCHEMATICS


Overall putting every thing together the difference between STOCK ANDROID and ROOTED ANDROID is the range of access.In latter you have more access and thus you can  do more modification and unleash the power of ANDROID and in prior case you just need to use what developers want you to access, even after shelling out some 10K- 20K for your device.

If you have any DOUBT,ADDITIVES  or CORRECTIONS  let them flow in comments.

Next part is about pros and cons of rooting.