Why is this option not simply the default then?
I can't say for sure, but I'm guessing because Ken wants people to think about how they want to do this. The passthrough option seems to work reasonably well, but it is doing pretty funky stuff under the hood. The other methods that use a Makefile.PL also have their drawbacks, so it's really up to each developer to decide how they want to handle this.
For something that wants to replace an existing module, I find the lack of migration paths a major deficiency.
Somebody else has created a Makefile.PL => Build.PL converter tat works for simple Makefile.PL scripts. If you're doing something complex in your Makefile.PL, there's obviously no way to automate the conversion.