You have added yourself to the number of people that prefer the standard (or Classic) transport and electronics to the later Sankyo transport and electronics. (of which, I am one, BTW). Even though the CR-3 has a direct drive capstan & slaved, vs both off a separate motor & belt driven on the LX-5, as well as further tape guides and "less" accurate head tracking, the sound from the older decks just seem more live and real, IMHO. Of course, you HAVE to be assured, via testing, that both decks are operating within their specs, which on untested decks is a total crapshoot. You may have a superb CR-3, poorly adjusted, and an ok LX-5, operating at it's max. But I have done a lot of post restortion comparisons of superb condition units of both, & the LX-5 ( and its autoreversing higher optioned cousin the RX-505) and ZX-7, & all have the same playback signature, where there actually appears to be more depth to the sound stage, and a solid distinct bass line. On the CR-3/4/5 the sound is all there, but sounds flatter, dimensionally, and I agree the bass is a slight bit boomier & less focused. Unless you A/B them side by side, it is not something you would notice, I think.
Lapis likes to use warm analog vs cold digital, but when I compare a CD to a tape onthe CR series, it is not cold to me, but still better sounding (less fatiguing) on the tape. As you noticed the older decks were built with a standard 1V output, vs the .75V on later decks (or even .5V on still later ones) and I think that also helps. When I test decks, I play a 400Hz 0dB test tape in each and adjust the output via a T-100 to assure equal footing at -5dB. The CR3/4/5/7 do have marginally better W&F, but their smaller capstan shafts seem to negate the gains a DD would profer, whereas the ZX-9 and Dragons, with their LX-5 sized capstans, normally provide a more significantly lower W&F than the CR-3/4/5/7.