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One issue that can happen that the article didn't mention is running out of AST node identifiers in Clang.

Clang uses a 32-bit number to identify AST nodes. If a single translation unit is large enough, it can overflow this and you can get some very weird compilation errors.

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Unless your amalgamated source file is getting into the 100s of megabytes to gigabytes range, I doubt that would be an issue.

If template instantiations use up AST node identifiers (I don't know whether whether they do), I can see scenarios where crazy amplified template instantiation chains can eat substantial chunks of that range.

They do.

I suspect extensive use of Boost-style template metaprogramming is a great help in making this goal realistic.

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