I spotted the new v110 on Humble Bundle and downloaded it. At first, I was put off because it had the same behavior as before, but I caught the words "Translocated Process" in the crash report for ModLauncher and dug further.
I believe that the problem I have run into is
App Translocation, an irritating security feature added to macOS 10.12 and later that randomizes execution paths in certain circumstances. Because Soma keeps resources outside of the app bundle, this meant that launching it through the GUI (which translocated it) caused the paths to those resources to break.
As per the article linked above, I removed the quarantine attribute by entering the following into Terminal:
xattr -d com.apple.quarantine /Applications/SOMA/Soma.app/
...and voila, the game runs when launched normally. Earlier HB releases also launch when treated in this fashion.
Best of all, v110 includes the Safe Mode update! Thank you for being so active and responsive.
To help with developing a wider fix (if one is necessary, it's unclear if others are having this issue), my installation process is simply to download the Humble Bundle .zip through Transmission/Safari, decompress it using Archive Utility, and drag the whole folder into Applications in Finder; a very standard flow. It may be that the quarantine bit is not getting flipped when dragging Soma into Applications because it is nested inside another folder, but that's unclear. Without needlessly reorganizing the resources, a workaround may be to use Humble Bundle's "Additional Content" field to describe the quarantine removal command; some other games in my library do this for additional installation information.