Changing fonts via setfont or dosfont both stop being in effect upon CLS. I would continue to investigate that, but I also noticed that it did not change the height of the DOSBox window - no screen mode change, number of lines, font height..
In Windows it's 80x25 (rows/cols) by default in a command prompt, and it is as well under DOS, but in DOS and DOSBox it seems to stretch those 25 lines to the virtual screen, rather than adjust the screen to match the font height at 25 lines.
If I attempt to change the DOSBox window resolution from the default "original" (which I presume is 640x480, as selecting that produces no change) to 640x200 (I use ykhwong's build, and it allows on-the-fly changing of resolution), which should be a bit less than half the height, it does not produce a 640-wide screen, and instead seems to adjust to some other smaller resolution, 320x200 it looks like, by eyeing it.
The font you provided, the 8x12MSI, looks very close to what I want when previewed, but unfortunately does not turn out that way when applied.
At this point I believe it to be futile, DOSBox doesn't seem to accept odd low-end resolutions, which would be required for the size of window of a command prompt on Windows NT+.
Thanks for the assistance in investigating this, and for the resources, though.