The reasons I always think of it as one system:
1) It was meant to have the CD from the beginning and was well supported, not some afterthought brought out years later.
2) The cd is just a storage medium, without additional cpu power, hardware scaling/rotation, etc.; even its save file and av capabilities could be added with other peripherals. Other than redbook and adpcm stuff, any game on cd could've been done on a huey.
3) Maybe it's tough for guys just starting out today, but for the longest time Duos were pretty cheap; it wasn't hard to find one for $150 or less, so why would anyone buy a base system to save less than $100? The whole reliability argument doesn't wash with me either, not when so many systems worked flawlessly for 15-20 years and gear changes, cap jobs, new blazing lazers, etc. were relatively cheap.
4) After years and years of playing the games, reading reviews, etc., I know which format most games are on. It's not something I have to think about or look up very often.
5) The most important reason is that the first system I bought was a TurboDuo. For me,format has always been a non-issue, other than knowing I couldn't play Arcade Card or Games Express games without the corresponding system cards and a region mod.