This is just a personal setting which I find works the best on my Lakland 5.
I find taking out the mids cleans up the sound in the mix with lower distortion.
On an active bass never run the volume flat out unless it's a temporary gain thing.
Volume = 8 <> 9
Treble = 7
Mid = 3
Bass = 7
what's your reason for not recording with the bass flat out? I can't seem to think of a reason not too! You should normally make sure that you ARE recording flat out with most things as it ensures that everything is running optimumly (ie good strong signals going between componants in the signal chain etc)
then again a bass circuit is so simple I've not known it to be too much of a problem unless the volume is RIGHT down.
Be careful of taking all those mids out of your bass signal, the mids are very important to a bass getting heard, in most mixes the highs will end up getting chopped off a bit but theres often a bit of mid work, a subtle boost etc, to make sure the bass can be heard in the mix. If you take out a lot of the mids your only choice is to put these back in unnaturally with a big eq boost! Wheras its a bit easier to cut it out if it's too much!
A big 'smily face' eq is flattering and fun to play with but is often not what you need to record.
That said, you are right that a mid heavy sound can easily clutter up a mix, its putting yet another signal into that all important mid area and you need a bit of skill to get it right! keep at it though.
if the mids being up is causing distortion then you're probably riding the gains a bit too high somewhere and the extra mid is pushing it over the edge! the loudest signal a bass can make should be no-where near distortion point for most good preamps (after a DI that is and most will be fine before as well!)