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We've had no issues using dotNet 4.6.1 with SmartAssembly 6.9 so far, sorry that the documentation doesn't yet reflect this. I'll see what I can do to get it updated.
"The assembly targets .Net Framework v4.6.1, which is not available on this computer. Install the associated .Net Framework to process this assembly."
Using the steps described in this KB article, I verified that .Net v4.6.1 is installed on that machine. The OS on the machine is Windows Server 2012 R2 (Standard).
Any suggestions on how I might proceed would be most welcome.
This seems like a more generic error message to do with problems with the .net installation, rather than applications using it. Are you able to try repairing your .net install?