I looked into it further, and it looks like the codebase actually does confiscate those outputs. For the sale of "simplicity," it applies the p2sh rules to all transactions in all blocks (including pre-P2SH blocks) except ones occurring in one specific block that they made a single exception for. Thus, the other exceptional outputs are now unspendable.
Source:

GitHub
bitcoin/src/validation.cpp at 13891a8a685d255cb13dd5018e3d5ccc18b07c34 · bitcoin/bitcoin
Bitcoin Core integration/staging tree. Contribute to bitcoin/bitcoin development by creating an account on GitHub.
