That's correct @MarcelTempelman the MR84 has 2 fixed radios, one for 2.4GHz and one for 5GHz, it does not have an XOR radio to support dual 5GHz if that's what you were referring to.
Also correct that there isn't a Meraki ANT part number with 4 leads, so on an MR84 you would use 2xANT-25 dual-band patch or 2xANT-27 dual-band sector antennas for example. Each of those antennas is dual-band 2x2. For an antenna with 4 leads, the 4x4 Aironet AIR-ANT2513P4M-N antenna is also supported, but that's a larger panel antenna for HD deployments like in stadiums, perhaps not ideal for warehouse aisles.
Thanks for pointing out the documentation not mentioning proper antenna separation, I'll bring that up to the documentation team. Ideally directional antennas would be at least a few wavelengths apart, so I wouldn't suggest placing them right next to one another, might be more aesthetically pleasing but definitely less effective.
I've designed several MR84 deployments with directional antennas like 25/27, but more typically in outdoor stadium type deployments and a few other use cases. As you said, for warehouse aisles, and wanting a single antenna element, and not needing 4x4:4, I agree with your direction to go with MR42E and likely either the E5 wide patch or F5 narrow patch antenna. Note the narrow patch is physically a larger antenna, much larger than the size of the AP, which might be a consideration but that's just the physics of a narrow patch.
Regards,
Dave