Default Multisite subdirectory installation...

Apologies in advance if this is out of scope but I'm basically grasping at straws so any assistance is appreciated.
I'm in the process of moving some WordPress multisites from an existing Godaddy shared hosting environment to a GoDaddy virtual dedicated server. The first thing I notice is that when attempting to perform new multisite installations on the new server I'm rarely given the option to select subdirectory as the prefererred installation. Instead I only have the option of creating sub-domain installation. I thought this was an issue with the new server but I get this when performing new installations on one of the existing shared hosting accounts. Since the sites resolve GoDaddy support points to WordPress. Am I missing something and is there a way to perform subdirectory installations?

Also, what applicable methods and suggestions are available for moving multisite installations between hosts?

Any responses appreciated.