So, two things solve this: adding this to forge.config.cjs:

rebuildConfig: { force: true, }, 

and adding a redo script between rebuild and make:

npm run build; 
npm run rebuild; 
npm run redo; 
npm run make; 

package.json:

"redo": "rm -rf node_modules/macos-alias/build && rm -rf node_modules/sqlite3/build && npm rebuild macos-alias && npm rebuild sqlite3"

(I was also having trouble with macos-alias throwing a fit saying it was compiled with a different version of node.)