Anyway to control Communities E-mail Welcome Message

This was an issue on a project I worked on as well. This particular feature is not very admin friendly (as you found out the hard way:). We chose to uncheck the "Send welcome email" box under Communities > Administration > Emails. We then created a workflow rule on the User object to send out the welcome email to new community users. The workflow rule fires on record creation only as has a criteria for "Profile EQUALS 'Your Community Profile Name(s)'".

You can use {!$Network.NetworkUrlForUserEmails} into Visualforce email template to send password setup Url of community and can set this template into community to send Welcome email to portal user, You can also handle on the basis of profiles etc into VF email template.