Unless I misunderstand your question #1, if you do not set the system lock to be on, in which case you cannot change anything, I believe the 990 actually works the way you want. Back when I got the 990 I sent a question to customer support about this because I was hoping it would revert back to the default, as I was experimenting with different modes. Scott said it does not. Changes you make on the fly to the active input change the default setting, so LAST is the default. The exception is where the 990 automatically detects and switches to DD5.1 or DTS or back to the default 2-channel (like PLII-Movie).

Scott at custrom support suggested using an unused video input for alternate set-ups for the same source to allow easier A/B switching.