... what is weird is that the basic dry tone of the bass seems different just by going through Mainstage. I am using Metric Halo interfaces and when I compare the signal right in the Metric Halo Console, it's much stronger and fuller sounding than the Mainstage tone.
With comparing
"right in the Metric Halo Console" do you mean a sort of "direct monitoring", where the incoming sound gets directly routed to an output? Can it be that for this routing the sound doesn't get converted to digital and back but rather remains analog? A straight analog in/out connection?
In this case and assuming that Mainstage alone does not change the digital sound you rather compared the analog to the digital sound, you tested the converters of the audio interface. In any digital processing you have one conversion at the audio input, then pure digital processing (or no processing) and another conversion in the interface to feed your speakers. Especially a bass can sound different after the two necessary conversions.
I suggest another test:
If your audio interface has ADAT in and out, just connect the ADAT out to the ADAT in and connect them via the console software. All you want is to convert to digital and back and hear the result.
If you don't have ADAT or other digital signal possibilities, route the signal through the computer. A fresh Logic project with nothing else than one audio channel does the job. Plug your bass or preamp into the MH interface, route it to Logic and from there back out. You can also use Soundflower, Jack, Plogue Bidule, Max MSP or whatever. All you need is to route the digital signal back to the audio interface.
The AD and DA conversion is what you want to hear. If the sound is different then you know what you can get from this interface. And this is what you can get in any software system.
Finally, compare the sound from the test above to the sound through Mainstage. With no other processing the two should be identical.