I am confident that your intuition is correct.
3rd Gens don't have raised rails, which that rack is designed to fit into.
With enough fabrication, anything can fit anything,
but I suggest finding something easier to start with.
Do you specifically want a basket-style rack?
For a few bucks more, I would suggest something like:
3rd Gen 4Runner Half Roof Rack | 1996-2002 4Runner | Sherpa Equipment Co.
That is designed to fit 3rd Gen track and is just as if not more useful.
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