I plan to chat with some folks about this. I'm hoping the full 1.0 release of Earthless isn't too far away from now - that'll be the version that features on the KEX port if they do update it.
noclipping through that window i look at just as the crash happens, and succesfully bypassing that spot as long as i keep my back turned to that window, i suspect it's a visplane error (though iirc chocolate would actually specify it was a visplane error so i don't get why it doesn't do so now?)
The NumLumps error generally appears if you load the mapset with -file instead of -merge. It's basically not loading some custom graphics correctly. Surprised you got 4 maps deep without seeing it. See if you can fiddle with your command line/launcher to use -merge.
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...and that this error does not, despite my memories of previous encounters, necessarily happen immediately on startup...