Yes, good point.
But best to configure things in whichever way best optimizes for the primary usage of the rig, I feel.. as long as I've clearly determined what that is. Of course I need to accommodate whatever inputs the recorder has.. unless modding that too, which is more extreme but has been done by some TS members. I don't go that far. My rigs used into handheld recorders use miniXLR up to the end of the signal chain where small right-angle stereo mini TRS plugs are needed to plug into the recorder.
To retain the ability to to use mini-jack equipped battery boxes or preamps, say as a backup or whatever, you can build short adapter cables to convert back to mini-plug/jack, and will only need to use them when using that alternate gear. That way the primary configuration remains optimized, but you have fallback options.
For instance, I've set things up both ways in the past using the DPA miniature mics that feature a built-in cable and terminate to a coaxial microdot connector. If I want to retain the microdot connectors on the mics I make up a female microdot to mini-XLR adapter cable (or to stereo miniplug or whatever). Whereas if I'm setting up the rig for specific regular use and optimizing for that, I'll cut off the dots, trim the mic cables to the most appropriate length and re-terminate directly to my preferred connector. In my current custom fitted four channel rig all four DPA mics terminate to a single multipin miniXLR and the four mic cables are of different lengths. That eliminates adapters and connections as well as the need to loop and secure excess mic cable length. But I waited until I knew I wasn't changing the rig further to do that.
If I build one of these with four channels it will be for use as a backup/higher-security-alternate to the mini-XLR input 4channel preamp I currently use.