Actually the 563A differs from the 45a in this regard. The 45a cannot do time alignment for SACD sources, whereas the 563A can. Both can do TA for all other sources. Another notable difference between the 563 and 45A is its BM characteristics :
the 563A has crossovers at 100 Hz (DVD,CD) 200 Hz (DVD-A) and 120 Hz (SACD),
-12 dB/octave rolloff slope for both high- and low-pass for all formats
The 45A has crossover set at 100 Hz for all formats, -12 dB/octave rolloff for the low pass for all formats, and the same for the high pass filter for all formats *except * SACD, where the high-pass slope changes to -6 dB /octave
(One upshot for both these players is that, using their bass management, different formats may sound different NOT because of SACD, DVD-A, or CD being inherently different-sounding, but because the players' BM treats them differently. This is the sort of thing that bugs me when people make claims about audible difference they attribute to the *formats* -- rarely do they report whether their systems are set up to treat each format the same. And of course, one might expect the two *players* to sound different from each other too, given the different ways they bass manage the same format)
These results are all from Sound & Vision's bench test results. There were other results for the 563a such as main vs surround channel noise, and channel overload characteristics, that may differ between the 45A and 563A. However, such tests were bit more detailed for the 563A than for the 45a, so a direct comparison may not be possible from the reports. The 45A results aren't online AFAIK, but the 563A results are -- see
563A bench test results
which was part of this review
563A review
I will try to remember to dig out the issue with the 45a results and post them if anhyone's interested.