Securing and Aligning Ballnuts

[JAZZCNC]

Am I right in thinking that none of these bolt holes are threaded and that through-bolts are used to secure the ballnut to the housing, which allows for a very small bit of alignment adjustment?

Yes small degree of adjustment can be made.

Can custom-machined housings be made to allow for a greater degree of adjustment?

It's Custom to your requirements so can be anything you like.!!

Also from what I've seen, the ex-stock ballnut housings seem to be a lot broader than many of the custom-machined housings... Is there a reason for this?

Not sure what you mean by Ex-stock has there are many designs and methods for ballnut housings.?