It's less a problem of  what some rules say than of fixing imperfect and incomplete rules for those who need detailed rules.

I didn't say it's all your fault, Unicornst.
However, the vendors are as well as the customers able to say what they want to have changed or why they do things in a certain way. Referring to some rules all the time doesn't work out well.
I know the "rules" and they don't say anything about unique file names, conventions, directory structures or databases.

Some ReRo people read this and can notify the responsible people of MP about the complaints.
They can change their rules or come with some reason why not to do it.
I write it here because in the end there will be different things that bother different people. A thread like this is a good place to write down all the wanted changes and all the complaints about what is going on.

"Someone who thinks logically provides a nice contrast to the real world." - someone said. :p*

There are vendors which do a good job with their products and files but some just mess things up. I won't give examples for good nor for bad vendors here.