The reason AC3 is at 48 kHz is that DVDs use a 48 kHz sample rate, as does BluRay (however, BluRay can accept higher sample rates for AC3). The first digital disc format, audio CDs, uses a 44.1 kHz sample rate because of limitations of late 1970s/early 1980s technology at the time it was invented. DVDs require a 48 kHz sample rate. You gain absolutely nothing by going to 44.1 kHz and someone could argue that you'll actually make the quality somewhat worse. 448 kbps is used because this is highest allowed bit rate for AC3 on DVD (BluRay allows higher). You can use a lower bit rate, but you'll be re-encoding and lessening the quality, even if you can't tell. But don't use 44.1 kHz. There's NO reason at all short of insanity for that. You could argue about saving space with lower bit rates, but lower sample rates won't save you any space.
Must you use AAC? AC3 is well supported and will be for years to come. Converting AC3 to AAC gains you nothing and any such conversions are lossy, even if you can't notice it. I don't deal with Handbrake and I avoid AAC where possible, so I have no idea what the Prologic II setting does.