The permissions saved in the Role Permissions Manager is saved in a table/doctype called Custom DocPerm. The child table in the DocType doctype is called DocPerm. By editing the doctype, you’re changing ERPNext configuration primitives - in this case the default permissions that ship with the doctype. It’s almost certainly not what you want.
This difference is poorly documented mostly because it’s not something most people are going to have to customize/build against. What is your desired outcome?
so u mean even the permission rule row in every doctype is of no use ? if all is handled by role permission manager ? so why to have that in first place ?
DocType permissions are maintained by developer(user who created the DocType), it is kind of default permission,
role permission manager permissions are maintained by system manager (Custom DocPerm), the first time role permission manager is opened system will auto fetch default permissions from DocType, it can be changed or new rules can be added as needed. these permissions override default permissions in DocType.
in other words if default permissions are Okay, no custom permissions needed, if you remove custom permissions, it will revert to default permissions.