Are you doing this with the OSD scripts or with Provisioning templates? They cover some of the same use cases, but are quite different tools underneath. Based on the option to hit the button to join a domain you are using OSD. I'll go with that unless you tell me otherwise.
Also, just to make sure we're on the same page, what version of LANDesk are you using? Major version and service pack, please.
1 - If you are on 9.0 SP2 or later I don't see why this would be a problem. It was a known issue on 9.0 with no SP and I don't remember if SP1 had it fixed or not. Let me know on this.
2 - This is expected behavior. The Windows sysprep process requires a key to know which version of Windows to be deployed in the situation where you have multiple images in a single file, or upgradeable images, etc. Their process is to use that info to match product, but assume that you have a KMS server setup to do the activation, which doesn't require a key. If you are using MAK licensing (which it sounds like you are) then this can cause a bit of a problem. More on that in number 3.
3 - If you want to auto activate I would recommend setting up a KMS server and doing it that way. Auditing is a lot easier and once it's setup it works automagically. If you want to activate individual machines using a Multiple Activation Key (MAK) licensing model you need to run the following commands post install:
cscript \windows\system32\slmgr.vbs -ipk <product key>
cscript \windows\system32\slmgr.vbs -ato
The first line applies the product key and the second line activates using that product key. You can make those changes in the sysprep file. It requires a manual edit if you are using the OSD tool. Let me know if you need help with that.