I do use JR extensively for Mch, but also for stereo. This issue has come up frequently, but I do not have all the answers for all system setups. I have commented on this more than a few times here.
Source Number of Channels may work in this case, but I have had problems with it so I do not use it. So, that should be tried with the Meridian to verify it works properly. Specifically, does the .1 input channel map properly to the .1 output channel so that the Meridian can use it in its bass management. If it works properly, then the OP's problems are all solved with one zone for stereo and 5.0 or 5.1 Mch. But, maybe not, so we would be back to zones and to avoiding Source Number of Channels in the DSP Studio output setting.
The potential problem centers around 5.0 vs 5.1 files. The Channels metadata = 5 for 5.0. But, Channels = 6 for 5.1, because Channels is an integer field. Testing will verify that the 6th channel goes out to the Meridian as the .1 = LFE channel or whether JRiver has "moved" it to a different output channel that the Meridian "sees" as a surround channel. Not sure.
In any case, here is what I do without any issues. My system feeds a Mch Exasound DAC via USB. (The Dirac Live VST plugin is embedded in JR.) I use bass management in JR Room Correction. I have two zones, one with fixed 5.1 output, another with 7.1. I use Zoneswitch to automatically switch based on the Channels tag in the input file >6. Both zones use 2.1 output automatically for stereo source material via the checkbox in DSP Studio. So, stereo plays as stereo, not "expanded" to Mch.
The only 7.1 material I have is on a few Blu-Ray videos, so for music, only the 5.1 zone is normally used, and I have no problems with playlists, as video watching is rare and not comingled with my music listening. Stereo plays as 2.1 stereo and Mch up to 5.1 plays properly. The 7.1 zone is switched in automatically as necessary on the occasional 7.1 video or rare 7.1 BD-A.
As a footnote, any 3.0 or 4.0 Mch recordings are created as 5 channel with the appropriate channels null. This is automatically done by SACD rip and extract tools. So, they play fine, too, in my 5.1 zone without artificially created channels, which is what I want.
Of course, hi rez plays as hi rez under the control of the output sampling rate conversions in DSP Studio.
Sorry to be so complicated. But, I am perfectly happy with my system setup.