No, and the reason it chose that one is not clever at all.
The env-var scan matches API_URL as a substring, so SIM_AGENT_API_URL is a candidate on equal footing with NEXT_PUBLIC_API_URL. The base URL is then assigned first-wins in file order. Line 40 beats line 79. Nothing ranks the canonical names above an arbitrary prefixed one, and nothing tells you in the report that there was more than one candidate.
Open issue, no fix yet, and no override flag. The workaround is to correct api.baseUrl in projects/<slug>/envs/<env>.yaml after applying — it is one line per environment and the file is yours from then on, so this is a one-time cost rather than a recurring one.
The thing to actually guard against is not noticing. Read the envs block in --report-only before you apply, and if the app has more than one *_API_URL in its env files, assume the guess is wrong until you have checked it.