Your first point is spot on. PerlMonks Discussion is a separate section based more on topic than on type of discourse (you can argue that it is for "meta discussions", but that is only partly true). But I also find that the bleed-over is quite low so it makes for a good section division.
Your second point is completely bollocks, however. "Perl" did not used to mean "just Perl 5". Besides the obvious case of Perl 4 existing (and Perl 1, and lots of different versions of Perl 5 and lots of different distributions of each of those versions), we have discussions of Perl modules, Perl programming techniques, Perl on Win32 or Perl under Unix-like systems, Perl for GUIs, Perl one-liners, things only tangentially (or less) related to Perl, etc.
Having a section for Perl one-liners would not work well. Sure, most Perl "scripts" you come across can be easily categorized as either a one-liner or not. That doesn't mean that most discussions either only talk about one-liners or never talk about one-liners.
Similarly, any given Perl script either offers a GUI or doesn't. But a large number of discussions cover both GUI and explicitly non-GUI topics in the same discussion. And there are tons of topics that are neither "GUI related" nor "non-GUI".
There will be questions that are strictly restricted to Perl 5 and questions that are strictly restricted to Perl 6. But there will be a lot more questions that either aren't explicitly about either one or that explicitly address both.
In your scheme, into what section does one post a question "Seeking wisdom on moving from Perl 5 to Perl 6"? "Difference between Perl 5 and Perl 6"?
The most common questions here boil down to "I'm trying to do $X". I suspect it will become quite common to get answers that include "... but if you use Perl 6, then you can ...". And even when that happens, it won't necessarily mean that the author of that answer is certain that the question's author isn't already using Perl 6. It will still be possible to write code that works just fine and identically between Perl 5 and Perl 6. Discussions are unlikely to be strictly "Perl 5" or strictly "Perl 6". Many will be "both" or "neither" and it will be quite hard to predict which of those categories the thread will eventually fall into.
There is a much clearer need here. We need the ability to declare that a particular example of Perl code only works in certain versions of Perl. "use 5.008; # Requires safe signals" is one existing tool for such. There are other tools specific to the Perl 5 vs Perl 6 boundary. And these tools are not specific to PerlMonks and should not be limited to PerlMonks.
Another tool that I very much like is quite simple. "perl5" (no spaces) and "perl6" (no spaces) are extremely useful for enabling searching and filtering of all kinds of things. Every search tool supports them (google, super search, "find on page", human eyes, etc.). Humans (and software) have no problem understanding them (despite Larry's worries about dropping the space from "Perl 6"). Please use those when appropriate.