I'm under the impression that very little is disclosed to us MD-buying public about the quality of pre-recorded MDs, so I can't say much on that. I don't think they necessarily use better equipment...
Here's a couple potential answers that I came up with.
First distant possibility is that the laser beam reflecting off a pre-recorded disc is stronger than that of a recordable disc (IIRC). This is just how the discs are. Some will argue that this "laser power" is often key to the sound quality of all "optical" formats. e.g. an old unit may sound less stellar than when it was brand new. And dust may help make your deck perform not-so-stellarly...
So based on that theory, if you have a pre-recorded disc and a recordable disc, both with the same ATRAC data, one may sound better than the other.
Another distant possibility is that the source that is the data source for pre-recorded MDs is not in 16-bit, but 20-bit or 24-bit. MD as an audio format, IIRC, is not strictly defined as 16-bit in terms of audio data. IIRC (again), if you have a 20-bit or 24-bit sound source, and your MD deck accepts 20- or 24-bit input as-is, ATRAC will be able to reap the benefits of that
to an extent.
Also, because ATRAC does some kind of "bit-shifting" during the encoding, some people consider ATRAC to have 20-bit accuracy at least for the low frequencies, and say this is why portables use 20-bit D/A A/D conversion. If you go to MDCP and check out the JA3ES deck interview, it mentions this bit-shift.
It seems that very few consumer equipments seem to accept non-16-bit inputs. And they're often the most expensive home decks. The D/A converter of some other decks are set so that the top or bottom 4 bits get automatically get truncated.
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So I can't really answer the pre-recorded Q...
But there's often a cost advantage in buying decks over portable recorders. Let's say, getting a Sony 470 (or the old 440) over the R909 recorder. Could save you enough to get a couple EX70s to impress the family stockings.
In the past this advantage was even bigger, because pre-R909 Sony portables didn't have type-R, but the decks like the 440 did. I remember when I was in the US I saw the 440 selling for less than half of what I'd spent for the R900.