I can't speak from experience about the 52, but the DAB54 is an excellent bit of kit. I bought one in 2004 for my '98 A3, and I've still got it now, it's hopped from car-to-car because I can't really find anything to trump it on features that are important to me.
I've never used an FM/DAB splitter - I've used a glass-mount (basically
*THIS* setup), and a roof-mount AM/FM/DAB combi aerial. The former worked just fine and delivered good reception in moderate and greater signal areas. The only problem was that it was an absolute ball-ache to fit to the A3; so much so that I gave up. I couldn't stick it on the windscreen as the wipers would clip it, didn't want to have slack-cable to the rear side-windows could still be opened, and it didn't look likely there'd be a flat enough patch away from the sweep of the rear wiper at the back - although I couldn't be certain, a larger problem for me at the rear window was the roof spoiler my A3 had.
It was on the A3 I used a Blaupunkt branded AM/FM/DAB combi antenna, roof-mounted to completely replace the OEM AM/FM aerial and its base. Drawbacks here - it wasn't far off £100 for the antenna at the time, and pulling the headlining down to lay the cables is a bit daunting (and work that some just might not want to do). Advantages, performance was absolutely brilliant, and the car pretty much retained its factory looks (the angle of the mast was slightly different to OEM).
From what I read, the FM/DAB splitters ARE NOT compatbile with amplified aerials - which would suggest they wouldn't work with the A3.
Probably the best thing you can do is have a look at, or even speak to
dabonwheels.co.uk - I've dealt with them a lot and they've never failed to impress me; they're extrememly knowledgeable, take a very much no-bull approach (clear product performance ratings etc), and have always bent over backwards in the customer service department. There's a pretty comprehensive range of aerials on their site, it's probably worth having a read through them.
As regards your other queries - SD cards - beware, SD card compatibility is one thing that these head units are a bit quirky with; I've got a 1GB card that works fine in my DAB54, but I'm aware not all do. I used to work with a firm who dealt with Blaupunkt and I know they used to keep a compatbility list, but I doubt that's up to date any more. Probably the only thing to do is try...
You don't have to bypass the rear amp - you can use the line-outs on the DAB52/54 to feed it, and the HU's internal amplifier for the fronts (as the OEM HU does). I can't remember off the top of my head for certain (will be checking soon as the DAB54 is going in my B5 in the not too distant), but I've a sneaky feeling that the pin-outs are all the same, therefore not requiring a harness adapter. That said, if my memory has failed me, I'm certain there's an adapter out there...
...which could also be useful on the other issue - swapping the permantent and ignition live lines... Basically with a car radio you've got a permanent live, which as the name suggests, is always fed from the battery, meaning your radio/EQ presets etc. stay in the radio's memory; the ignition live is (again as the name suggests) only hot when the ignition is on (or until the key is removed following ignition-off); this is what controls the HU's ability to turn itself on and off as you do the key. It's common for the position of these required by aftermarket radios to be the opposite of that on the car's wiring loom. It's not a complicated task to switch them around (perhaps just cut-in and stick some spade connectors (or similar) in the lines so you can swap and swap back as you like); but as mentioned, a harness adapter might be helpful here as often they've already got connectors on the lines so you can swap them, or if not and you have to modifiy it yourself, you're not actually hacking at the car's wiring in any way.
All the best,
Rob.