sidechaining volume question

If you adjust the make-up gain—may be called Output on some compressors—so that the overall perceived volume of the bass is about the same with and without compression, do you still have this problem?

When you are using the sonitus gate to sidechain-duck, if you've set it up correctly its input meter shows the side chain signal (kick drum or whatever you choose to use).
You can automate the threshold (the little slider between the two meters) to control the amout of pump you are applying to the bassline without affecting the actual volume of the bass line at all. If you raise the slider right to the top (and above the signal) the effect goes away and gradually gets stronger as you lower the slider back into the kick drums signal. 
If your kick drums signal is near or reaching 0db inside the gate then lower it some (lower the fader on the kick drum track itself) because it doesnt need to be that strong to act as a sidechain signal. As long as the kick is peaking around -6 to -12 inside the gate then you have that bit of space above its signal peak in which you can raise the slider out of the signal, and the bassline will chug along un pumped. Lower the slider back into the signal and the bassline starts pumping again.
Always give the gate its own Bus and set the ouput signal of the bassline to that Bus.  Don't make the mistake of inserting the gate on the bass lines track because that is messy for various reasons and also the gates automation envelope starts getting in the way of track automation etc. With the gate on its own bus anything you want to send to that Bus gets pumped too.
Incidentally, its also possible to then use an Aux send on other tracks to send a partial signal to the gates bus, so you could have a bassline heavily pumping and a synth pad lightly pumping, both of them utilising a single instance of gate. 
 Aux sending does though obviously tend to change the percieved level of the signal somewhat so its not the preferred method for basslines.
I use both methods at different times, but for Basslines I  use the threshold slider because it gives precise control and nice pump fades as you slide it. 

No problem, although having just read my own post I notice I got slightly mixed up and forgot the depth slider! (I was away from sonar pc also)
Still pretty much what I said but use the threshold slider to on/off the pumping and use the depth slider if you wish to vary the degree of effect.