As far as tone, the differences in woods, primarily in the neck but also in the body, will effect the tone and sustain.
Sustain is especially affected by neck woods, with ebony neck lams having the most noticeable effect. Purpleheart is also a popular choice for adding more sustain to a neck.
In my view, there is, for instance, a noticeable difference in tone between two basses that are the same except that one bass has Walnut top and back body lams and the other bass has Maple.
The main difference in the electronics will be that the CVQ at its highest setting will boost the cutoff frequency by 15db, where the top boost on the 3-way Q switch on the Series I is 9db, thus at 15db it is louder at the cutoff frequency and has a different tone.
As for output, check the positions of the preamp gains, the two outside trim pots mounted on the control cavity plates. It could be that these trims are at different settings on the two basses.
Other factors that affect both tone and output are pickup height and strings.
Now that I think about it, different woods may also effect output. If I recall correctly, woods, rather than adding to tone, actually filter out different frequencies.
And then of course ears; differences in output level are often accompanies by perceived differences in tone, ie louder sounds better.