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Would any problems develop with indexing (or with anything else) if I decided to make the invalid pages transitional and keep the rest strict? Is it ok to have a mix of XHTML 1.0 Strict and XHTML 1.0 Transitional on a single site?
No spider actually reads the doctype or takes it into account when reading the page - the doctype is useful only for ensuring the correct rendering mode in the browser, as well as for the validation process.