If you're serious about x64 deploy and hosting, you need to let people change that setting in an automated way.
The basic problem here is developer might need to change that setting a lot while he/she experiments compatibility. Sometimes you have components which cannot run in x64 mode, sometimes you just compiled for x86 and thus you cannot run x64 until you recompile. Sometimes you want to run x64.
If user / developer can change this at will, that would be a very good feature. For hoster who want to have control over this setting, it could simply become part of plan feature, the same way PHP or ASP.NET are and so it could be enabled or disabled by hoster. Once enabled for a plan, user should be able to switch by simply logging on DNP.
That would be the best way to do that. I'm mixed about ticket or message: users would already do that anyway so it doesn't sound very useful.
Take care.