Kalle pinged me the other day (last monday to be exact!) to let me know that he had upgraded the versions of Lib-V (SFT encoding/decoding library, for ISVs interested in SFT capabilities in their own software) and SFT Encoder which now include full App-V 4.6 support!
More information at http://www.gridmetric.com/ .
Also Kalle pointed me over to a blog he posted which helps in understanding the usage scenarios for SFT Encoder, http://www.virtualisointi.fi/en/archives/212 it also explains mass-migration to 4.6 with it and processing GUI.
As always remember that the third party tools are not managed or supported by Microsoft.