The flaws you mention are inherent in Optical Character Recognition (OCR) indexing. For newspapers arranged in columns there really is no way to train the OCR program to recognize the column arrangement in order to add proximity searches. This can be done with other types of text.
Ancestry.com definitely is not going to undertake manual newspaper-page indexing. The search engine at NewspaperArchive.com, the source of much of the newspaper material on Ancestry.com, is superior, but that site has its own faults.