How do you skip the transfer purchases step when syncing iPod touch?

You can't disable that feature. It is designed that way so you won't lose the content on the ipad if it is stored in iTunes on your computer. If you continue to sync, the purchases will continue to be transferred.

Unticking sync apps will remove apps that are already installed on the ipad via the sync process. You can ask the question 10 more times - but you can't turn that off - if you sync your ipad.

If you want to manually manage music on the ipad - you should be able to do that without transferring the purchases - but you can't sync without transferring purchases. This article describes manually managing music. Don't let the title fool you.