I think a MOTU 16a is a more economical choice than a 24ao and 24ai unless you need the extra channels.
Yes, you can route all the audio into JRiver for DSP and then back out with the MOTU drivers. However, you have to use the ASIO Line-in which isn't easily accessible with a remote or app. You can leave the HTPC always on, though, and have a Zone on ASIO Line-in mode. Use the other Zones for playback from the HTPC.
You will have some latency on the audio, but should be able to delay video in the Atmos processor. You can also use a display with high latency, like the JVC projectors that have ~140 ms of latency.
This doesn't apply to you since you want to use active crossovers, but others might find it helpful. Another option to consider that I recently helped someone implement is to use a Yamaha CX-A5100 processor as the processor and DAC. This is cheaper than a 24ao/24ai yet still uses the 32-bit ESS Sabre chips. It also is rated for the same voltage output. It can do Atmos 5.1.4, but not 7.1.4.
The Yamaha is a lot like JRiver in that it can have multiple DSP Presets and you can even combine manual EQ with the YPAO -RSC room correction. It also has the most extensive set of measurements I've seen for integrating the Atmos speakers. You can access all the setting on the Yamaha with a computer and web application which makes setup easier than with other processors.
In the system I helped with, Dolby TrueHD content is bitstreamed to the receiver. It is then decoded by the receiver and has the appropriate DSP applied. All other content on the HTPC (music, DVD, Blu-ray with DTS-HD) is processed by JRiver and uses JRiver's DSP and is then sent on to the Yamaha as PCM with no further DSP applied.