To play devil's advocate, were there any (perceived) benefits to this
arrangement when originally introduced, other than not needing the
SWIG binary to compile Python bindings?

That predates the start of my involvement with GDAL, so my guess would be that this was just what you mention: for the sake of simplicity of people building GDAL, at a time where its only build requirement was the basic tools autoconf, make and g++. Nowadays, getting SWIG isn't harder than getting PROJ or any of the "optional" dependencies you generally want to make a reasonably feature complete GDAL build.

Even

--
http://www.spatialys.com
My software is free, but my time generally not.

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