Starting back in the late 90's, it became the norm for analog inputs to be converted to digital automatically. It started around the time that digital processing (Dolby Digital and DTS, bass management, and so forth) became so widely used and expected. In many cases, it was impossible to avoid this A/D process, but the ability to defeat it by selecting an analog bypass mode soon came about. I would expect any modern surround processor will convert steroe analog inputs to the digital domain unless the user selects a bypass mode. The 990 does offer such a mode, and you can configure an input to make this process take place automatically any time the input is active. If you have a very high quality analog source, I'd suggest giving this mode a try. On the other hand, the A/D/A process has proven to be remarkably transparent in my experience (using it with the 7.1 direct input on DVD-Audio and SACD sources) - the 990 may be able to run the signal over to digital and back more cleanly than you might expect. Even with that transparency, I'd still probably go with the analog bypass.
The 990's 7.1 direct input's do offer the ability to run through the digital bass management, but the input does not pass through any other processing. As a result, you cannot apply any surround processing (Pro Logic IIx, DTS NEO:6, or anything else) to that input.
I expect that the 5380 chip was selected when Etronics developed the Sherwood P-965 platform (the basis for the Outlaw 990). As long as the chip (which seems to have been a great performer in the 990) is available, I would see no problem with using it. Chips like this have pretty long service lives - Analog Devices may be pushing a newer (and therefore more expensive) chip to customers developing new products, but they'll want to keep older designs in production at the same time to satisfy customers like Etronics and Outlaw. Look at Cirrus for example - the 990 is using their 49400 processor, but there are still products out there using its predecessor even while the Cirrus has a successor to the 49400 in production.
You can set different crossover points for the side surrounds and rear surrounds, but I am not sure about setting the rear surrounds to large unless the side surrounds are also set that way. It's been a while since I messed with it, so I could be remembering incorrectly, but I think the rear surrounds would only set to "small" or "none" if the side surrounds were small.
Let us know if you have any other questions - the 990 is a great product, and there is a pretty good crowd around here to help you out.