See manual page 43.

The option:
SETUP / Options / Device Mode/DSD / Dig. Out Source: Main out
lets the Digital out signal follow the output 1/2.

In general it‘s better to have the main speakers connected to the subs, otherwise bass management would not work as intended by the manufacturer.
Even the whole MiniDSP optimization wouldn’t have access to the main speakers, so would probably yield unexpected and sub-optimal results.

The main point with digital filter processing is the latency of the whole process.

If you run the subs only through such, their signal is delayed relative to the mains, the bass will lag behind the rest.

Low pass filter alone (digital or analog, no matter) already delays the bass.
This is not desirable, the result is no smooth transition between sub and mains, and a slow sounding bass.

Of course, something comes out, but where is the improvement?

Better to have all signals run through MiniDSP if it’s meant to do room correction and bass integration.

Doesn't TMFX/RoomEQ also allow for delays to compensate for distances?  This can also be used for latency compensation. 

The MiniDSP (specifically the 2x4 and 2x4HD) are regularly and religiously used for multi sub optimization (MSO plugin) "Post AVR" using Sub outs - and then the AVR lines everything up via distance/delay settings to be in-phase and perfectly aligned.  I'm assuming TMFX can also do that (I'd hope so if a cheap AVR can).  This is very very common in Home Theater land where insanely powerful sub setups/arrays are used and expertly integrated together and with mains.  You don't have to use the crossover in the MiniDSP (but you can), but you will CERTAINLY use the biquad or FIR filters to integrate multiple subs together for a uniform response - each sub with specific filtering strategically applied.

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