There is nothing happening at one month, and nothing “locks” permalinks. There is no actual difference in the system, the only difference is in the initial multisite configuration interface.
When you first define WP_ALLOW_MULTISITE to true, and visit the network screen, you get the initial setup menu which lets you set up the configuration. It looks much like this here:
http://codex.wordpress.org/File:network-create.png
On that screen, if you have had your installation single site longer than 1 month, then it won’t let you pick a “subdirectory” setup.
And that’s it. That’s the only difference.
In the end, it doesn’t actually matter. It’s going to give you some defines to add to the config file anyway, and if you tell it subdomain = false, then it will be subdirectory.
What are they doing to fix that? Why, nothing at all. This is intentional and part of the system. If you override it, then it works fine anyway. In the long run, the difference between subdirectory and subdomain should disappear anyway with domain mapping support, but this is purely an interface thing to prevent people from accidentally doing something stupid and breaking their site.
This in no way relates to your other question, because you are not using multisite.