I was changing the way my domains forward today and I have folders set up at godaddy.
ie... .ca, .com, .misc, personal etc.
The personal domains go to a number of businesses of mine and between them there are probably 80 or so custom set domains with special name server settings, mx records etc.
THe other folders belong to my domaining business.
I changed hundreds of domains in seconds and never once had to worry about my customized domains.
I thought to myself.... "My god it does not get any easier than that"
Compared to the other registrars I use the GoDaddy bulk tools are absolutely golden.
So I'm not answering the OP's question but I'm wondering why he would be looking for a godaddy alternative, the tools and services are getting better and better there.