I think that some 990 owners have found that in their case they are using nothing but digital input, which is probably where the comment "why use analog" comes from - for them, it didn't provide a benefit. Heck, until I hooked up the SMS-1 recently I didn't really have any analog sources to think about.
As I understand it, Outlaw is fully aware of the bug in the bass management and is working on both a software fix and some sort of official summary of exactly what is currently going on with the 990's bass management. As I mentioned in another thread recently, I contacted Outlaw directly earlier this week to try to put together a summary of how the bass management was designed (which as you have discovered gets complex when you try to look at all scenarios) to help everybody around here understand what is going on. I was told that an official statement was going to be more appropriate (something that would more clearly run down the issue rather than add to the "running around"). Based on that, I feel comfortable saying that they are actively working on this issue and plan to give all of us exactly the sort of confirmation/summary you are looking for.