Hi,
From the bug report discussion you referenced:
"
The workaround ("solution", really) to this is to change the password for the affected user to a post-4.1 hash.
"
If that does not work and you need to set some sort of option, just create a PDO instance yourself, configured it the way you like it and pass this PDO object to R::setup(),
RedBeanPHP will accept the PDO object as its connection.
Let us know if this works.
Cheers,
Gabor