After getting help from others in the official Godot discord, I solved this problem by recompiling the web assembly templates in an earlier version of emscripten. I used 3.1.48 after reading this reddit post and it resulted in a different error about dynamic linking not enabled. Not the best, but still progress!
According to the help received from the discord, when compiling from source, it’s apparently a good idea to use the exact version of Emscripten that was used for the official build. The exact version, noted in the 3.5.3 documentation, is 1.39+. I’m going to experiment further with which specific version works, but that solved my initial problem. The very latest versions of Emscripten may easily break things in Godot.