Topping D90 bass bloat?

I think your issue is related to the output gain setting.  On APOS' page it says:

The Topping D90 digital-to-analog converter (DAC) has a volume control function that can be disabled to make the D90 function as a DAC that produces output levels of 4Vrms (XLR) and 2Vrms (RCA). The default setting is the higher one, which has slightly better specs, and can overload the inputs with some preamplifiers or headphone amplifiers, resulting in distortion. Changing the D90SE's output to 4-volt XLR/2-volt RCA will usually solve the problem.

Try the different filter settings that the topping provides.  One might help. I have a few topping dacs, and they do tend to have a deep bass response. Also try some different cables between the dac and the preamp. 

@mattsaunders2000 is the topping brand new? If so, allow it 200hrs of continuous operation to digest the bean buns and see if it gets rid of that bloat. If not, return it or sell it. It’s probably just a terrible synergy. 

@dougsat , I did try the Topping in 'preamp' mode, which is how to engage the volume control that you refer to. Didn't notice a difference there to be honest, and with the ARC preamp in the mix, I don't love managing two separate gain dials. I elected to just keep the D90 in "direct dac" with a fixed volume. 

You know, this could be the opposite.  If the preamp impedance is too low, and DAC output impedance too high it can cause a source to have too little bass, and your Topping was actually producing the correct amount.  I'd be very surprised if this happened though. 

The Topping has a volume control so I would try connecting the Topping directly to the amplifier. Interesting to then listen to see if it still sounding bloated. Synergy in a system sometimes is elusive even when your mix of equipment is top notch. When you get it right you know it! Make sure if you do try this to turn the Topping volume down first and slowly bring it up. 

I can’t speak about your exact setup, but when changing out any components, we sometimes forget that we took a lot of time optimizing what we had to fit our taste. When you change things you need to spend some time integrating it into the system. Distance of speakers from walls, sub level adjustments, etc. And then you also have to accept the possibility that you might just prefer what you had to what you bought. All part of the hobby. And sometimes it’s just a matter of acclimating to the new addition. Good luck.