...I'd think a larger or more live room would sound really muddy....
Yup granted you will lose some definition. My thinking has been conditioned by recording and playing with my trio recently so please take all I say with a pinch of salt
The difference between a small room and a large room can be huge, but they can both behave in odd ways.
Close miking in a large space can be nice (just a hint of ambience) and relatively distant miking in a small room can be interesting too...just watch out for room resonances. The room I've been doing some practicing in recently has a resonant frequency activated by my drummers snare. can get pretty peaky on a recording.
You need to be clear what you want from a recording (creating an ambience, highlighting detail in presentation, a recording of a specific performance etc etc etc and of course a combination of all)
It seems you want everything equally presented (and why not

), so a close miked route is really the best option.
There will be compromises though and failure to achieve certain expectations. Something can always be "better", but don't fret. You're recording at that given moment with a given selection of equipment. It will only yield so much. Of course there are ways to counter certain short fallings, but these can come at a price. Ie warming up your bass might mean you lose some punch from the drums.
Remember you are recording the whole ensemble, not just your bass so something that sounds warmer in the flesh will have a different feel when coming from a pair of speakers on playback. (I regard this as a good thing, otherwise why play live?)
As I said the myspace tracks aren't bad at all apart from a rather thin and unnatural saxophone sound.