Here is my purist approach:
AVR "Pure Direct" Front Left/Front Right > Passive Stereo Selector Input > miniDSP > External Power Amplifier > Speakers
Other 2-channel Stereo Sources > Other Inputs on Passive Stereo Selector
This allows you to bypass the AVR processing for front left and right to the extent that it allows you to for video sources, and completely for front left and right channels from non-video sources.
To accommodate subwoofers, instruct the AVR that you have "No" Subwoofers (if applicable) and split the full-range passive stereo selector outputs to the sub(s) and to the external speaker miniDSPs. Set the miniDSPs' high pass filters, delays, levels and polarities to blend the mains with the subs.
Note that this configuration relies on full range audio to the front left and right, so that you are doing your own bass management for those channels, Set front speakers in the AVR as "Large" and all others as "Small." The AVR should still perform bass management for all other channels, sending center, surround and height channel bass to the front left and right outputs at frequencies below the frequency selected in the AVR, which in turn will be accommodated by the crossovers in the miniDSP units for the mains and the subs.
In the AVR's own delay settings, set delays for front left and right to minimum, and adjust delays for Center, Surrounds and Heights to accommodate the total delay introduced by the miniDSPs, which are in turn internally adjustable for the mains vs. the subs. (You will have to do acoustic measurements with a test mic for this, as the miniDSPs will add their own inherent delays to what is selected in their settings, and the subwoofer physical distance and internal delays must be accounted for.)
My approach basically treats all surround processing in the AVR as a sort of "sidechain" event apart from a straightforward 2-channel stereo system, as much as the AVR will allow. The downside is the added complexity of setup, including the loss of automatic room correction that the AVR could otherwise provide, unless you upgrade your mniDSPs to Dirac Live. Otherwise this requires manual external DSP setup for all channels, ideally, which is what I have done, simply because I "can't get no satisfaction" from what Dirac Live tries to do. I've tried it.
No one said this would be easy, and you have to ask yourself whether it's all worth it. Admittedly, for most it won't be.