Did you have any luck? I see the 2048 bit option just added under cPanel's CSR generation page in WHM. I'm pretty sure I didn't see this before. So, it looks like some work may be going towards this???
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I know this is a very old post, but I did find this thread doing a Google Search so if I found it other might as well, so might as well have some update info here.
As of the past several months just about ALL SSL Certificate vendors now ONLY issue 2048 bit certificates. If there still some that issue 1024 bit they will not for long.
With the 2048 bit certificates just about all 2048 bit Certificates require a Intermediate Certificate (chain certificate) to go with the the 3rd party SSL Certificate that you purchased. With a LOT of 1024 bit certificates expiring and coming up for renewal they will need to be replaced with 2048 bit certificates but give very little if any instructions that you will need to add the Intermediate Certificate before it will work properly.
We have and others have had much difficultly with cPanel trying to get the 2048 bit with the bundles installed correctly. Most of the time having to manually install the 2048 certificate with the CABundle.
Do your home work other wises your site you could start having a LOT of shopping cart abandonment when your customer sees SSL Certificate issues.