I've been digging through LinqToXSD and custom tool possibilities today and news aren't very satisfying..
LinqToXSD class generator to work well needs at least a configuration file to configure the namespace, however there is no way* to pass parameters to custom tool so no configuration at all is possible in this case. I thought about setting default parameters,
but that isn't really a good option too.
For me generating classes manually using LinqToXSD console tool and a batch file is now the easiest working solution.
* - at least any way I know and I've been investigating this a bit today. If anyone can prove me wrong I'll be happy to hear about it.