Just specifying $Using:exclude in the Where-Object cmdlet doesn't work because it is in a nested scriptblock.
In your case , the Using:folder works because it is a local variable directly passed to the Invoke-Command scriptblock.
But "Using:exclude is passed to a scriptblock for Where-Object, which is itself nested inside the scriptblock for Invoke-Command.
$Using allows to pass local variables to scriptblocks only one level deep, not to scriptblocks nested any further.
This behaviour is not specific to the Where-Object scriptblock, any cmdlet which has a parameter taking a scriptblock behaves like this when it is inside a Invoke-Command scriptblock.
Unfortunately, I don't think this behaviour is documented.
By uncommenting $Using:exclude at the beginning of the Invoke-Command scriptblock, you are effectively declaring the variable $exclude inside the remote session.
So, in this case, $exclude becomes a local variable inside the Invoke-Command scriptblock and can be passed one level further, to the nested Where-Object scriptblock.
That's why it works when you uncomment $Using:exclude at the beginning of the Invoke-Command scriptblock, it's a workaround for the behaviour of $Using.
For the official help information about this run :
Get-Help about_remote_variables -Full