There's no direct benefit from using a PCIe 4.0 x 4 in a PCIe 3.0 x 4 slot. The only benefit would be future upgradability.

 

I would strongly recommend to install the OS on the SSD drive, as it will greatly improve boot time and overall response of the operating system.

At the same time I would caution you and be ready for possible windows 10 activation issues. Pending on what you change to your system, windows might think this is a different system and need reactivation. If I am not mistaken Alienware provides OEM versions of windows 10, not retail versions.

And if I am not mistaken windows 10 OEM activation has changed from windows 7 OEM activation, and each OEM now requires a unique digital license. Gone are the days of the OEM keys being stored on the machines and being able to reinstall and activate the OS as many times as you like.

My R10 came with windows home and a digital license linked to my Microsoft account. Unless you have access to a legal method to activate a windows 10 installation, you might run into issues activating the OS.

 

https://support.microsoft.com/en-us/windows/activate-windows-10-c39005d4-95ee-b91e-b399-2820fda32227

 

Forgot to add you can freely download the windows 10 installation media directly from Microsoft:

https://www.microsoft.com/en-us/software-download/windows10

 

Using the DELL recovery environment will likely not allow you to reinstall the OS to another drive and move the activation over. 

 

Agreed, if your OS is on the HDD, and you're adding a Samsung M2 NVME PCiE drive, then definitely put the OS on the SSD.  Even your boot time will be immensely impacted.  

You shouldn't experience any activation issues, the digital activation is stored on MS servers by motherboard.  I haven't seen a SSD/HDD upgrade on the same motherboard trigger an activation issue so long as you clean install the exact same version of windows.  You can also backup image and restore to the new SSD if you prefer (although I'd usually recommend a clean install).