Have raised a subscription Support Request on this.....
As to the original individual transparency selection annoyance, this is the reply received from Autodesk Support
"...You are right, Thanks for reporting this... I will report this as a regression from last version.
I have crossed check with some Map3D specialist but there seems no good workaround at the moment.
Sorry for that..."
Probably be fixed in 2013 now.....
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