There will never be such thing as a restriction of where a plugin can place a link that will display a certain page the plugin is registering.
It’s just in your scenario that a plugin is registering a settings page and the link normally is named settings as well.
As there is no convention or suggestion what plugin authors can/should do, I see it even more probelmatic to restrict this. I doubt that a restriction would be technically effective and on the social side, it will only create problems for those who want/need to circumvent some more restricted approach.
This has various reasons and you are totally right, this can be a problem because it’s not easy to locate all the plugins settings.
For the plugins I code that actually have a settings page, I prefer them to add in the plugin listing – at least as well. I know that some users look there if they don’t locate stuff within the menu.
So it would be nice if core provides an additional routine plugin authors could call to register their settings page. For plugins that don’t do that, the plugin listing could display a greyed out – no settings – or else remark.
Because I know that not all plugin authors do announce their settings page at least in the plugins listing, I’ve create a quicksearch plugin for the admin that let’s you browse the menu quickly: Admin Quicksearch (WordPress Plugin) – It let’s you search the plugin listing quickly as well.